Epidemiologic and Other Analyses of 

HPAI-Affected Poultry Flocks 

1 June 2023 Interim Report 

Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Suggested bibliographic citation for this report: 

Center for Epidemiology and Animal Health. (2023). Epidemiologic and other analyses of HPAI-affected 

poultry flocks: 1 June 2023 Interim Report. U.S. Department of Agriculture, Animal and Plant Health 

Inspection Service. https://www.aphis.usda.gov/aphis/ourfocus/animalhealth/animal-diseaseinformation/avian/avian-influenza/hpai-home/hpai 

For more information, contact: 

Amy Delgado, MS DVM PhD 

Director, Center for Epidemiology and Animal Health 

USDA: APHIS: Veterinary Services 

Center for Epidemiology and Animal Health 

2150 Centre Avenue, Bldg. B-2E7, Fort Collins, CO, 80526-8117 

Phone (970) 494-7302 

Email: Amy.H.Delgado@usda.gov 

Web: http://www.aphis.usda.gov/animal-health/ceah 

The U.S. Department of Agriculture (USDA) prohibits 

discrimination in all its programs and activities on the basis of 

race, color, national origin, age, disability, and where applicable, 

sex, marital status, familial status, parental status, religion, sexual 

orientation, genetic information, political beliefs, reprisal, or 

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(202) 720-2600 (voice and TDD).

To file a complaint of discrimination, write USDA, Director, Office 

of Civil Rights, 1400 Independence Avenue, SW, Washington, DC 

20250-9410 or call (800) 795-3272 or (202) 720-6382 (TDD). 

USDA is an equal opportunity provider and employer. 

Mention of companies or commercial products does not imply 

recommendation or endorsement by the U.S. Department of 

Agriculture over others not mentioned. USDA neither guarantees 

nor warrants the standard of any product mentioned. Product 

names are mentioned solely to report factually on available data 

and to provide specific information. 

USDA–APHIS–VS–S&P–CEAH 

NRRC Building B, M.S. 2W4 

2150 Centre Avenue 

Fort Collins, CO 80526-8117 

(970) 494-7000

Email: vs.ceah@aphis.usda.gov 

http://www.aphis.usda.gov/about_aphis/programs_ 

offices/veterinary_services/ceah.shtml 

(June 2023) 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Table of Contents 

Executive Summary .............................................................................................................................1 

Introduction ........................................................................................................................................3 

A. Description of Outbreak.......................................................................................................................... 3 

B. Comparison of 2022–2023 HPAI Outbreak to 2015 HPAI Outbreak....................................................... 7 

Phylogenetic Analysis and Diagnostics ...............................................................................................10 

A. Phylogenetic Analyses........................................................................................................................... 10 

B. Public Health Aspects............................................................................................................................ 12 

C. General Influenza A Diagnostics and Characterization......................................................................... 12 

Epidemiologic Studies to Investigate the H5N1 Virus in WOAH Poultry [Commercial] and WOAH 

Poultry [Backyard] in the United States ......................................................................................14 

A. Table Egg Production Case-Control Study............................................................................................. 14 

B. Turkey Case Control Study .................................................................................................................... 18 

C. Turkey Case-Control Study Economic Analysis ..................................................................................... 22 

D. Turkey and Table Egg Study Weather Analysis ..................................................................................... 22 

Estimating the Time of H5N1 HPAI Introduction Into WOAH Poultry [Commercial] Flocks Using 

Diagnostic Test Results and Production Data ..............................................................................25 

A. Summary ............................................................................................................................................... 25 

B. Results................................................................................................................................................... 25 

C. Discussion.............................................................................................................................................. 30 

Avian Influenza Surveillance in Wild Birds ..........................................................................................31 

A. Background ........................................................................................................................................... 31 

B. Wild Bird Surveillance Program ............................................................................................................ 32 

C. Morbidity/Mortality Sampling .............................................................................................................. 33 

D. HPAI Detections in Mammals ............................................................................................................... 34 

Modeling Avian Influenza Transmission at the Interface of Wild Birds and Domestic Poultry...............36 

A. Background ........................................................................................................................................... 36 

B. Methods................................................................................................................................................ 36 

C. Preliminary Results ............................................................................................................................... 37 

D. Next Steps ............................................................................................................................................. 38 

Analysis of BirdCast and e-Bird Migration Data: Implications for Disease Introduction, Spread, and 

Prevention.................................................................................................................................39 

A. Potential Use of BirdCast Data for Awareness to Enhance Prevention Measures ............................... 39 

B. eBird Output of Relative Abundance of Migrating Birds ...................................................................... 41 

References ........................................................................................................................................43 

Acknowledgments.............................................................................................................................45 

Appendix A: Detailed Outbreak Overview by Flyway ..........................................................................46 

Appendix B: Initial Contact Epidemiological Report ............................................................................58 

Appendix C: Commercial Turkey Case Control Survey .........................................................................65 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Appendix D: H5N1 HPAI Bird Detections.............................................................................................84 

Appendix E: Time of Introduction Modeling Methods.........................................................................87 

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List of Tables and Figures 

Table 1. Confirmed detections of highly pathogenic avian influenza by production type and World 

Organisation for Animal Health (WOAH) reportable species as of 31 March 2023 ...................................... 6 

Table 2. Major genotypes and gene constellation ............................................................................................. 11 

Table 3. Estimated odds ratios, and their 95% confidence intervals, of an operation being positive for each 

of the variables included in the best fitting exact multiple logistic regression model. Also included are 

the p-values for the tests that the effect size is non-zero ........................................................................... 16 

Table 4. Estimated odds ratios, and their 95% confidence intervals, of an operation being positive for each 

of the variables included in Bayesian model averaging. Also included are the estimated probabilities 

that the effect size is non-zero .................................................................................................................... 16 

Table 5. Results of multivariable logistic regression analysis of factors associated with HPAI H5N1 infection 

on U.S. WOAH poultry [commercial] meat turkey farms ............................................................................ 21 

Table 6. Results of univariate conditional logistic regression analysis of weather factors associated with 

Table 7. Results of univariate conditional logistic regression analysis of weather factors associated with 

Table 8. Number of H5N1 HPAI detections from apparently healthy wild birds sampled by USDA–APHIS–WS 

between 1 June 2022 and 31 March 2023................................................................................................... 32 

Table A1. Confirmed detections of highly pathogenic avian influenza by State as of 31 March 2023........................56 

March 2023...........................................................................................................................................................84 

Table E1. Input prior distribution parameters used in the ABC approach to estimate the adequate contact rate 

HPAI H5N1 infection on U.S. WOAH poultry [commercial] turkey farms.................................................... 24 

HPAI H5N1 infection on U.S. WOAH poultry [commercial] layer farms ...................................................... 24 

Table D1. Number of H5N1 HPAI detections in apparently healthy and sick/dead birds from 1 June 2022 to 31 

and time of virus introduction for WOAH poultry [commercial] meat turkey flocks...........................................87 

Figure 1. Counties with highly pathogenic avian influenza detections in poultry by month and by flyway as 

of 31 March 2023........................................................................................................................................... 4 

Figure 2. Monthly highly pathogenic avian influenza detections by premises type as of 31 March 2023........... 5 

Figure 3. Bird map of HPAI-affected counties by North American flyway and premises type as of 31 March 

2023. .............................................................................................................................................................. 7 

Figure 4. Epidemiological curve of flock/herd inventory [cumulative count by incident year] and count of 

Figure 5. Genotype distribution as (A) total counts and (B) proportion of all detections from December 

Figure 6. U.S. States with farms that participated in the 2022 HPAI H5N1 WOAH poultry [commercial] table 

Figure 7. U.S. States with farms that participated in the 2022 HPAI H5N1 WOAH poultry [commercial] meat 

Figure 8. Definition of hazard and control periods used in the WOAH poultry [commercial] turkey and table 

Figure 9. Relative timeline for time of introduction analysis by State, phylogenetic cluster, production type, 

Figure 10. Time from estimated HPAI introduction to detection by production type and likely source of 

premises affected by week of confirmed diagnosis date as of 31 March 2023 ............................................ 9 

2021 to 31 March 2023 in wild birds and mammals, left, and commercial poultry, right .......................... 12 

egg case-control study................................................................................................................................. 15 

turkey case-control study ............................................................................................................................ 20 

egg study weather analyses......................................................................................................................... 23 

and likely source of introduction. ................................................................................................................ 27 

introduction. ................................................................................................................................................ 28 

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Figure 11. Estimated adequate contact rate by production type and likely source of introduction, estimated 

by time of introduction analysis .................................................................................................................. 29 

Figure 12. Basic reproduction number (R0) by production type and likely source of introduction, estimated 

by time of introduction analysis .................................................................................................................. 30 

Figure 13. Map depicting the four primary North American waterfowl flyways ................................................ 32 

Figure 14. Number of H5N1 HPAI detections in wild bird species tested between 1 June 2022 and 31 March 

2023. State totals include detections from both apparently healthy birds and sick/dead birds sampled as 

part of morbidity/mortality investigations.................................................................................................... 34 

Figure 15. Detections of HPAI in mammals as of 31 March 2023 ...................................................................... 35 

Figure 16. Model-predicted risk of avian influenza spillover from wild waterfowl to domestic poultry across 

Figure 17. Distribution of risk values across all counties (grey bars) for each week of the year in which 

spillover events occurred. Red lines indicate the risk level for counties that actually had spillover 

the contiguous United States during four selected weeks of the year ....................................................... 37 

events........................................................................................................................................................... 38 

Figure 18. BirdCast Live Bird Migration Map of 22 September 2022 at 22:10 ET .............................................. 39 

Figure 19. H5N1 HPAI clade 2.3.4.4b virus of genotype B1.2 detections in WOAH poultry [commercial] and 

WOAH poultry [backyard] from April 2022 to March 2023 identified as IWBI. .......................................... 40 

Figure 20. Overlapping 15 July 2021 through 31 March 2022 and 15 July 2022 through 31 March 2023, 

BirdCast’s highest daily number of millions of birds in flight by day is shown over daily counts of H5 

July 2022 and 31 March 2023...................................................................................................................... 41 

Figure 21. Maps pulled from eBird Status and Trends in the U.S. for the week of 21 September 2022, 

Figure A1. Weekly confirmed detections of highly pathogenic avian influenza by reportable species and wild 

and H5N1 HPAI detections in wild birds, WOAH non-poultry, and WOAH poultry premises between 15 

focused on the relative abundance of blue-winged teal, Canada goose, and mallard species................... 42 

migratory bird flyways as of 31 March 2023 ........................................................................................................55 

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EXECUTIVE SUMMARY 

In January 2022, clade 2.3.4.4b H5N1 highly pathogenic avian influenza (HPAI) was reported in a wild bird 

sample from Colleton County, South Carolina. This heralded what is currently the largest avian influenza 

outbreak in U.S. history, involving many wild bird species and virus reassortments, with spillover into 

poultry, as well as wild and captive wild mammals and outdoor domestic cats. By March 31, 2023, HPAI was 

confirmed in 47 States including 323 WOAH1 poultry [commercial], 120 WOAH poultry [backyard], 370 

WOAH non-poultry, and 4 WOAH poultry [live bird market] premises. The primary driver for the spatial 

extent of the 2022–2023 HPAI outbreak has been migratory wild bird movements, with premises 

traditionally considered WOAH poultry [backyard] and WOAH non-poultry premises comprising the highest 

proportion of detections. 

Phylogenetic analysis of viruses from this outbreak has highlighted many of the unique viral characteristics 

influencing this outbreak. Examination of the available wild bird, domestic bird, and poultry sequences 

determined that at least 83 percent of U.S. detections in domestic birds and poultry are consistent with 

independent point source (wild bird origin) introductions. Many genotypes have been identified, with the 

major genotypes appearing in both wild bird and poultry detections, highlighting the critical role of wild 

bird-related spread in this outbreak. And as of 31 March 2023, 154 cases of infected wild mammals across 

17 species, as well as outdoor cats from Nebraska, Oregon, and Wyoming, have been reported. In the U.S., 

nearly all viruses characterized from mammals are Eurasian/North American reassortants and are often 

representative of the predominant circulating genotype at the time of detection. To date, there has been no 

conclusive evidence of sustained transmission between mammals in the U.S. 

To explore factors associated with spillover infection from wild birds to domestic poultry, case-control 

studies for H5N1 HPAI were conducted among WOAH poultry [commercial] table egg layer, pullet, and 

breeder bird farms, as well as WOAH poultry [commercial] turkey farms. Location within an existing control 

zone was a significant farm-level risk factor for HPAI on both WOAH poultry [commercial] table egg and 

turkey farms, highlighting the need for increased biosecurity and surveillance vigilance once a detection 

occurs in an area. Other important risk factors for table egg layer farms included the presence/sighting of 

wild waterfowl in surrounding areas, having feed or feed ingredients accessible to wild birds, the absence of 

a farm gate, and lack of personnel assigned to specific barns. For turkey farms, other factors associated with 

increased odds of H5N1 HPAI infection included having both brooder and grower turkey production on the 

farm, having toms as the sex market type, seeing wild waterfowl or shorebirds in the closest field, and the 

use of rendering for dead bird disposal. Factors with a protective effect included workers entering the 

selected barn using a shower at least some of the time and having a restroom facility available to crews who 

visit the farm. The economic analysis found that there are differences between case and control turkey 

farms in terms of on-farm biosecurity and investments. Control farms had statistically significant higher 

monthly biosecurity costs than case farms, and control farms also spent more on temporary biosecurity 

measures, such as gates, parking areas, temporary wild bird mitigations, temporary air intake inlet covers, or 

temporary vehicle wash stations. Importantly, case farms were 87.7 percent more likely to have plans to 

make permanent changes to biosecurity. Weather variables, such as precipitation, temperature, and 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

average wind speed have also been identified as potential risk factors of interest, and further analysis of 

weather-related variables is ongoing. 

The United States Department of Agriculture Animal and Plant Health Inspection Service (USDA–APHIS) used 

the HPAI National Model to support budget and resource planning, as well as to evaluate alternative control 

strategies and options. As the outbreak continued, disease spread and control modeling were used to help 

inform data-driven response strategies and resource allocation. Other modeling approaches were also used 

to inform the response and improve our understanding of disease transmission. Time of introduction models 

use diagnostic testing, daily mortality, and water consumption data to predict the time of virus entry into a 

flock. Analysis of data from 53 WOAH poultry [commercial] premises found that time to first positive sample 

varied by production type, introduction route, and reason for testing (median of 6 days for farms under 

surveillance and 8 days for farms passively reported due to clinical signs). The average adequate contact rate 

(see Appendix E, Table E1 for more information) across all premises was 4.9 contacts per day. In addition, 

the average number of secondary infections caused by a typical infectious individual over its entire 

infectious period when introduced into a completely susceptible population, as described by the overall 

mean basic reproductive number (R0) value, was 13.5 (range 2–62), which would ensure rapid spread 

through a barn. This work highlighted the value of closely monitoring mortality, water consumption, and egg 

production to quickly identify disease issues in the flock, while recognizing that these factors may vary, so 

understanding the trends within each production setting is important. 

The U.S. National Surveillance Plan for Highly Pathogenic Avian Influenza in Wild Birds was developed to 

maximize our ability to detect influenza A virus (IAV) in wild waterfowl. Between 30 December 2021 and 31 

March 2023, over 40,000 apparently healthy wild waterfowl were sampled and tested for IAV using realtime reverse transcriptase polymerase chain reaction (rRT-PCR). Overall, targeted surveillance and 

morbidity/mortality investigations of sick or dead birds have resulted in 6,086 detections of H5N1 HPAI 

lineage virus in over 130 wild bird species across 49 States, plus Washington, D.C. 

To better understand the risk of virus spillover from wild to domestic birds, USDA–APHIS collaborated with 

the University of Maryland and the U.S. Geological Survey, Eastern Ecological Science Center to model 

spatio-temporal trends in transmission between wild waterfowl and domestic poultry. Data from the current 

outbreak were used to evaluate preliminary model performance. Using data through January 2023, we 

showed that the model performed well at predicting county-level avian influenza virus spillover risk. Model 

results are now available online for poultry owner use to better understand their own risk context. 

Other valuable tools for understanding disease risk are eBird and BirdCast migration data. BirdCast 

migration maps show real-time intensities of nocturnal bird migration between local sunset to sunrise, as 

detected by the U.S. weather surveillance radar network. eBird is a database of species-specific, crowdsourced observational data by scientists and birding enthusiasts. Intense periods of bird migration, as seen 

by BirdCast maps, were correlated with outbreaks in domestic poultry, suggesting that this tool can be used 

to increase awareness of heightened HPAI risk due to wild bird movements. Using eBird data, we estimated 

that HPAI-positive premises were more likely to be detected within the first seven days of heavy wild bird 

observation within a 50 km spatial window. 

Further information on the epidemiologic features of this outbreak and additional analyses will be provided 

in subsequent reports and peer-reviewed scientific manuscripts. 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

INTRODUCTION 

In response to the Eurasian clade 2.3.4.4b H5N1 HPAI outbreaks in WOAH poultry2 [commercial]3 and 

WOAH poultry [backyard] across the U.S., USDA–APHIS–Veterinary Services (VS), APHIS Wildlife Services 

(WS), and the affected States have initiated epidemiologic, genetic, and wildlife investigations. These 

investigations will help provide a better understanding of factors associated with avian influenza virus 

transmission and introduction into poultry flocks. 

These investigations include the following: 

• Virus phylogenetic analyses; 

• A case-control study in turkey farms examining epidemiologic and economic factors affecting HPAI 

risk; 

• A case control study in table egg layer farms examining risk factors for HPAI; 

• A case-crossover study to examine associations between weather variables (e.g., wind speed, relative 

humidity, precipitation, temperature) and HPAI infection on commercial poultry farms; 

• Analysis of barn-level egg production and mortality records; 

• Analysis of waterfowl surveillance; 

• Modeling the risk of avian influenza virus transmission from wild waterfowl to domestic poultry across 

the contiguous United States; and 

• Analysis of the utility of publicly available data on wild bird migration for predicting increased risk of 

HPAI spillover to domestic poultry. 

To provide producers, industry, and other stakeholders with relevant epidemiologic information, this report 

includes the results from these investigations. 

A. Description of Outbreak 

USDA–APHIS identified the Eurasian clade 2.3.4.4b H5N1 HPAI on 13 January 2022 in a wild bird in Colleton 

County, South Carolina (Animal and Plant Health Inspection Service [APHIS], 2022). This detection was the 

first Eurasian H5 HPAI detected in the U.S. since December 2016, and followed ongoing reports of clade 

2.3.4.4b H5N1 HPAI in Europe (Freath et al., 2022) starting 27 October 2021 for the migration season (note 

that ancestors of clade 2.3.4.4b have been circulating along Eurasian flyways since 2017) and in Canada 

(WAHIS, 2023) starting on 4 November 2021. For Europe, Canada, and the U.S., wild bird detections have 

preceded detections in domestic poultry. Figure 1 describes the temporospatial detections of clade 2.3.4.4b 

H5N1 HPAI virus in domestic poultry in the U.S. (see Phylogenetic Analysis and Diagnostics section for more 

details). 

2 https://www.woah.org/en/what-we-do/standards/codes-and-manuals/terrestrial-code-onlineaccess/?id=169&L=1&htmfile=glossaire.htm#terme_volailles 

3 https://www.ecfr.gov/current/title-9/chapter-I/subchapter-B/part56#:~:text=The%20poultry%20are%20from%3A,with%20at%20least%205%2C000%20birds. 

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Figure 1. Counties with highly pathogenic avian influenza detections in poultry by month and by flyway as of 31 March 

2023. 

The first detection of HPAI in a domestic poultry premises occurred on 7 February 2022 on a commercial 

meat turkey bird operation in Dubois County, Indiana, and 14 additional detections occurred later that same 

month. These cases represented the beginning of a wave of detections in the U.S. (Figure 2) that 

corresponded with wild bird migration (see Analysis of BirdCast and e-Bird Migration Data: Implications for 

Disease Introduction, Spread, and Prevention section for more details). In March 2022, the number of cases 

rapidly increased to 87 detections confirmed by the National Veterinary Services Laboratory (NVSL). In April 

2022, the NVSL confirmed 166 cases of HPAI; this was the highest number of cases confirmed in a single 

month. In May 2022, a relative decline was observed with 89 cases confirmed by the NVSL. This was the first 

month in which the combined number of detections among premises considered WOAH poultry [backyard] 

and WOAH non-poultry exceeded the number of WOAH poultry [commercial] detections. 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Figure 2. Monthly highly pathogenic avian influenza detections by premises type as of 31 March 2023. 

Over the summer months, the number of confirmed cases sharply declined (Figure 2). The NVSL confirmed 

an average of 21 (range: 20–22) cases in June, July, and August 2022. Most of these cases occurred among 

WOAH poultry and WOAH non-poultry premises along the Pacific Flyway. 

From September 2022 through December 2022, the U.S. observed an increase in the number of confirmed 

HPAI cases per month (average: 75 cases, range: 62–93; Figure 2). These detections were likely associated 

with the fall wild bird migration (see Analysis of BirdCast and e-Bird Migration Data: Implications for Disease 

Introduction, Spread, and Prevention section for more details). Fall cases peaked in October 2022 with 93 

confirmed detections. Although the number of WOAH poultry [commercial] detections increased during the 

fall wave, the number of combined detections among WOAH poultry [backyard] and WOAH non-poultry 

premises continued to exceed the number of WOAH poultry [commercial] detections. 

In January 2023, the NVSL confirmed 28 HPAI detections, predominantly among WOAH non-poultry 

premises. While this reflects a decline from the number of cases observed during the fall wave, the number 

of cases soon began to increase again with 31 detections confirmed in February 2023 and 40 detections 

confirmed in March 2023 (Figure 2). These detections in February and March also included detections within 

WOAH poultry [live bird market] premises. 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Table 1. Confirmed detections of highly pathogenic avian influenza by production type and World Organisation for 

Animal Health (WOAH) reportable species as of 31 March 2023. Chicken Turkey 

Duck 

Pheasant 

Goose 

Other* 

Production Type 

WOAH Poultry 

Commercial Broiler Production 14 

Commercial Broiler Breeder Pullets 2 

Commercial Broiler Breeder 11 

Commercial Table Egg Layer 30 

Commercial Table Egg Pullets 4 

Commercial Table Egg Breeder 3 

Commercial Turkey Meat Bird 209 

Commercial Turkey Breeder Hens 11 

Commercial Turkey Replacement Hens 2 

Commercial Turkey Poult Supplier 1 

Commercial Turkey Breeder Toms 2 

Commercial Duck Meat Bird 7 

Commercial Duck Breeder 10 

Commercial Upland Gamebird Producer 16 

Commercial Breeder Operation 1 

Live Bird Market 2 2 

Backyard 49 2 15 5 2 47 

WOAH Non-Poultry 250 2 31 3 10 74 

Total 365 228 63 24 13 124 

*Other species includes assorted pet birds, chukars, ratites, multiple poultry species, and “other poultry” designations. 

As of 31 March 2023, the NVSL has confirmed HPAI detections in 47 States. These NVSL-confirmed 

detections included 323 WOAH poultry [commercial], 120 WOAH poultry, 370 WOAH non-poultry, and 4 

WOAH poultry [live bird market] premises. WOAH poultry [commercial] detections included 225 turkey, 37 

table egg, 27 broiler, 17 duck, 16 upland gamebird, and 1 goose premises (Table 1). Split by wild bird 

migratory flyways, detections included 180 premises in the Atlantic Flyway, 267 premises in the Mississippi 

Flyway, 175 premises in the Central Flyway, and 195 premises in the Pacific Flyway. The contribution of 

WOAH poultry [commercial] premises to the total number of detections was higher for the inland flyways 

than coastal flyways (Figure 3). Along the Mississippi and Central Flyways, WOAH poultry [commercial] 

premises accounted for 55 percent (147 out of 267) and 50 percent (87 out of 175) of detections, 

respectively. In contrast, WOAH poultry [commercial] premises only accounted for 28 percent (51 out of 

180) of detections in the Atlantic Flyway and 20 percent (38 out of 195) of detections in the Pacific Flyway. 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Figure 3. Bird map of HPAI-affected counties by North American flyway and premises type as of 31 March 2023. 

Phylogenetic analysis indicates most detections are the result of independent wild bird introductions (see 

Phylogenetic Analysis and Diagnostics section for more details). Premises traditionally considered as WOAH 

poultry [backyard] and WOAH non-poultry comprise the highest proportion of detections; these premises 

generally have lower biosecurity practices, with increased risk of exposure to wild birds. While WOAH 

poultry [commercial] premises continue to be at risk, with clusters of lateral spread observed following an 

independent wild bird introduction, transmission from WOAH non-poultry premises to WOAH poultry 

[commercial] premises has not been documented. 

A more detailed outbreak overview chronologically describing detections by wild bird migratory flyways, 

States, and production types is provided in Appendix A: Detailed Outbreak Overview by Flyway. 

B. Comparison of 2022–2023 HPAI Outbreak to 2015 HPAI Outbreak 

The primary driver for the spatial extent of the 2022–2023 HPAI outbreak has been migratory wild bird 

movements. The first poultry detection was in the Mississippi Flyway, which followed earlier detections in 

wild birds along the Atlantic Flyway. The virus then moved through the migration patterns in and out of 

Canada through the Atlantic, Central, and Pacific Flyways into Alaska. While the 2015 HPAI outbreak was 

initially preceded by migratory wild bird movements, disease spread was more heavily influenced by lateral 

transmission between farms after virus introduction to the Midwest, with farm-to-farm spread associated 

with the movement of people, equipment, and materials between premises. Unlike the 2022–2023 HPAI 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

outbreak, in the 2015 outbreak, the virus was introduced into the Pacific Flyway, moved eastward as far as 

Indiana, and there were no detections in the Atlantic Flyway. 

Given the expanded geographic range and extent of viral shedding in wild birds, it is not surprising that at 

least 83 percent of premises affected in the 2022–2023 HPAI outbreak have been consistent with 

independent wild bird introductions, shaping the spatial distribution of cases seen at the county level in 

Figure 3. Although many more counties have been impacted by HPAI in 2022 and 2023, compared to 2015, 

many of these counties represent a very small number of cases with no further spread between farms. This 

shift may suggest that improvements in biosecurity on farms and increased messaging around the 

importance of proactive measures to reduce the spread between locations have had a positive impact on 

limiting lateral transmission of virus. 

The broad geographic extent of this outbreak has had serious impacts on resource requirements for 

response. USDA–APHIS personnel began deploying to the first HPAI detection in February 2022 and have 

continued to deploy through drafting this report. More than 892 USDA–APHIS personnel and contractors 

have been deployed in support of the response, representing over 2,399 deployments as of 31 March 2023. 

The distribution of farm types impacted over the course of the past outbreak has also differed. In 

comparison to the 2015 HPAI outbreak, which only had 21 WOAH poultry [backyard] and WOAH non-poultry 

flocks impacted, the 2022–2023 HPAI outbreak has confirmed 490 WOAH poultry [backyard] and WOAH 

non-poultry flocks as of 31 March 2023. This likely reflects an increase in the prevalence of the virus in wild 

birds across all migratory flyways. To promote awareness of HPAI, the USDA expanded messaging on the 

importance of reporting disease among WOAH poultry [backyard] and WOAH non-poultry flocks and 

distributed information through social media outlets. During the COVID-19 pandemic, the number of 

individuals engaged in rearing chickens as a hobby and egg source increased exponentially (Lesley, 2021). 

Infections of WOAH poultry [backyard] and WOAH non-poultry flocks often serve as indicators of the 

presence of virus among wild birds, but in this outbreak, as with the 2015 outbreak, they do not seem to 

play a role in the epidemiology of the outbreak overall. There has been no evidence to support transmission 

of virus spread from WOAH poultry [backyard] or WOAH non-poultry flocks to WOAH poultry [commercial] 

based on epidemiologic and phylogenetic analysis (see Phylogenetic Analysis and Diagnostics section for 

more details). 

Figure 4 shows a comparison of the epidemiologic curves and number of birds lost or depopulated due to 

disease between the two outbreaks. A higher number of cases, in addition to an increase in the number of 

birds affected in the 2022–2023 HPAI outbreak, are reflective of increased detections of HPAI in WOAH 

poultry [backyard] or WOAH non-poultry flocks, as previously noted. As the current outbreak continues to 

evolve, additional comparisons and lessons learned between the two outbreaks are underway. USDA–APHIS 

has made numerous changes to response processes in a concerted effort to improve efficiency in control 

activities, indemnity and virus elimination payments, and repopulation processes and timelines. Initial 

estimates suggest that significant improvements have been made in all aforementioned areas, and more 

detailed information will be provided in the final epidemiologic report for this outbreak. 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Figure 4. Epidemiological curve of flock/herd inventory [cumulative count by incident year] and count of premises 

affected by week of confirmed diagnosis date as of 31 March 2023. 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

PHYLOGENETIC ANALYSIS AND DIAGNOSTICS 

A. Phylogenetic Analyses 

The 2022–2023 H5N1 clade 2.3.4.4b HPAI outbreak has surpassed the 2014–2015 H5 clade 2.3.4.4c 

outbreak as the largest animal health emergency in U.S. history (Figure 4) (Animal and Plant Health 

Inspection Service [APHIS], 2023), involving many wild bird species and virus reassortments (Animal and 

Plant Health Inspection Service [APHIS], n.d.), with spillover into poultry, as well as wild and captive wild 

mammals and feral domestic cats. Ongoing phylogenetic and biologic analysis has been conducted by the 

NVSL (Ames, IA; national and international reference laboratory for influenza A virus in animals) in close 

collaboration with USDA–APHIS–WS and the USDA Agricultural Research Services Southeast Poultry 

Research Laboratory (ARS–SEPRL; international collaboration center for influenza A virus). High throughput, 

near real-time full genome sequence analysis was leveraged by sequencing samples directly; the data 

pipeline includes RAxML to generate phylogenetic trees and generating tables of single nucleotide 

polymorphisms (SNPs) created using the vSNP pipeline.

4 Analysis of the available wild bird, domestic bird, 

and poultry sequences determined that at least 83 percent of analyzed U.S. detections in domestic birds and 

poultry are consistent with independent point source (wild-bird origin) introductions. 

The H5N1 clade 2.3.4.4b genotype A1 was first identified in wild birds collected in December 2021. 

Genotype A1 spread across all four flyways and reassortants with North American (AM) wild bird avian 

influenza viruses first identified in February 2022. Reassortant viruses account for at least 87 percent of 

viruses with several genotypes (Youk et al., 2023) spilling over into domestic birds and poultry; however, 

reassortment of the neuraminidase gene has been rare and has not been sustained to date. Several fully 

Eurasian H5N1 clade 2.3.4.4b introductions have since been identified following initial detection of genotype 

A1 in December 2021––genotype A2 was detected in February 2022 in the northeastern US and A3 was 

likely introduced via the Pacific Flyway in April 2022. Three additional introductions have since been 

identified in wild bird samples collected from October 2022 through December 2022––A4 via the Pacific 

flyway in wild birds in Alaska and A5 and A6 via Atlantic flyway (of note, A6 is a fully Eurasian virus with a 

reassorted neuraminidase (H5N5)). Reports in wild birds, domestic birds, poultry, and mammals extend into 

Central and South America as of fall 2022. 

In May 2022, HPAI was confirmed in a red fox in Rock County, Wisconsin, and by the end of March 2023, 154 

wild mammals across 17 species (Animal and Plant Health Inspection Service [APHIS], 2023a), as well as 

outdoor cats in Nebraska, Oregon, and Wyoming, had been reported. In the U.S., nearly all HPAI viruses 

characterized from mammals are Eurasian/North American reassortants and are often representative of the 

predominant circulating genotype at the time of detection. To date, there has been no conclusive evidence 

of sustained transmission between mammals in the U.S. E627K, a molecular marker in the PB2 gene 

previously associated with adaptation in mammals has been identified in seven foxes, two raccoons, three 

skunks, a grizzly bear, a black bear, and a harbor seal (only one of several characterized), from different 

States and genotypes as of 30 March 2023. The change from E to K in position 627 of the PB2 segment 

happens during virus replication in a mammalian species. While mammals are largely considered dead-end 

hosts, transmission from mammal to bird cannot be ruled out when E627K is present. The E627K marker has 

4 https://github.com/USDA-VS/vSNP 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

been identified in two wild birds as of 30 March 2023––a red-tailed hawk and a turkey vulture, both species 

likely to predate or scavenge on small mammals. The mutation has also been identified in eight WOAH nonpoultry flocks (one of which has a matching virus from a skunk found on the property) and one WOAH 

poultry [commercial] turkey flock. Other mammalian-associated mutations of interest (T271A, D701N) have 

been detected in a handful of viruses, largely from mammals and raptor species. Representative poultry and 

mammal sequences have been uploaded to a public database.5 Major genotypes (Youk et al., 2023) and 

their geographic lineage (Eurasian or North American) are listed in Table 2. Their prevalence in wild birds 

and WOAH poultry [commercial] premises is shown in Figure 5. 

NOTE: The outcomes of phylogenetic analysis should be interpreted in context of all available 

virus and epidemiologic information and should not be used directly to infer transmission. 

Table 2. Major genotypes and gene constellation (ea = Eurasian segment, am = North American segment).6 

Segment Group 

Genotype PB2 PB1 PA HA NP NA M NS 

A1 ea1 ea1 ea1 ea1 ea1 ea1 ea1 ea1 

A2 ea2 ea2 ea2 ea2 ea2 ea2 ea2 ea2 

A3 ea3 ea3 ea3 ea3 ea3 ea3 ea3 ea3 

B1.1 am1.1 am1.1 ea1 ea1 am1.2 ea1 ea1 ea1 

B1.2 am1.1 am1.1 am1 ea1 am1.2 ea1 ea1 ea1 

B1.3 am1.3 am1.3 am1.2 ea1 am1.2 ea1 ea1 ea1 

B2.1 am1.2 ea1 ea1 ea1 am1.1 ea1 ea1 ea1 

B2.2 am1.2 ea1 ea1 ea1 am1.1 ea1 ea1 am1.2 

B3.1 am2.1 ea1 ea1 ea1 am1.4.1 ea1 ea1 ea1 

B3.2 am2.1 am1.2 ea1 ea1 am1.4.1 ea1 ea1 am1.1 

B4.1 am2.2 ea1 ea1 ea1 am1.3 ea1 ea1 ea1 

5 https://gisaid.org/ 

6 Youk et al., 2023 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Figure 5. Genotype distribution as (A) total counts and (B) proportion of all detections from December 2021 to 31 

March 2023 in wild birds and mammals, left, and commercial poultry, right. 

B. Public Health Aspects 

The NVSL rapidly shares genetic and biological materials in collaboration with the Influenza Division of the 

Centers for Disease Control and Prevention (CDC), USDA–APHIS–WS, USDA–ARS–SEPRL, and other key 

partners. Whole genome sequence data shared by NVSL is used to monitor the virus evolution and assess 

the risk to veterinary and public health based upon the presence/absence of specific amino acid 

substitutions or protein motifs. 

To date, there is one report of clade 2.3.4.4b H5N1 HPAI detection in humans in the U.S. The U.S. case 

involved bird depopulation at an affected site in Colorado and tested positive by PCR only on the day of 

depopulation; all other testing was negative. The CDC continues to monitor the situation closely for signs 

that the risk to human health has changed (World Health Organization, 2022). The health of response 

workers and on-farm personnel is monitored at the State level in cooperation with USDA–APHIS and the 

CDC. 

C. General Influenza A Diagnostics and Characterization 

Avian influenza subtypes H5 and H7 are reportable worldwide because of their potential for mutation to 

high pathogenicity during replication in poultry. The presence of basic amino acids at the cleavage site 

contribute to the mutation from low pathogenicity (LPAI) to high pathogenicity. Mechanisms by which 

H5/H7 mutate from LPAI to HPAI include the gradual accumulation of basic amino acids (AA), insertion of 

repeated basic AA, and insertion of non-homologous genetic material (only reported for H7 viruses). 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Molecular diagnostic tests for IAV are used across the U.S. National Animal Health Laboratory Network 

(NAHLN). The most sensitive and specific tool for influenza A detection is the Type A-specific rRT-PCR, which 

targets at least the matrix gene (IAV-M); this is the primary surveillance tool used and it provides a semiquantitative result. The NAHLN tests samples first by the IAV-M test and further by the NAHLN H5 and H7 

tests when IAV is detected. Genomic data also confirms that diagnostic assays are fit for purpose. In silico 

analysis via computational modeling approaches confirms high similarity between the H5N1 virus sequences 

and the relevant primers and probes used for the IAV and H5 diagnostic rRT-PCR tests. 

All poultry samples with a non-negative test result for IAV by either serology or PCR are forwarded to the 

NVSL for confirmatory testing. The NVSL uses molecular tools to determine the subtype and pathotype 

(LPAI vs. HPAI) directly from swab or tissue samples. Whole genome sequencing is conducted directly from 

samples and on all isolated viruses and select viruses may be further characterized by pathotype assay in 

specific pathogen-free chickens. Major genotypes and their lineage (Eurasian or North American) are listed 

in Table 2. Their prevalence in wild birds and WOAH poultry [commercial] premises is shown in Figure 5. 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

EPIDEMIOLOGIC STUDIES TO INVESTIGATE THE H5N1 VIRUS IN WOAH POULTRY 

[COMMERCIAL] AND WOAH POULTRY [BACKYARD] IN THE UNITED STATES 

A. Table Egg Production Case-Control Study 

BACKGROUND 

The commercial table egg sector has had the highest percentage of affected birds from WOAH 

poultry [commercial] operations in the 2022 U.S. HPAI H5N1 outbreak, with over 75 percent of 

affected birds from WOAH poultry [commercial] operations part of the commercial table egg 

production sector. 

Wild bird introductions were identified as the primary means of spread in the 2022–2023 outbreak, 

and to explore factors associated with spillover infection from wild birds to domestic poultry, a casecontrol study for H5N1 HPAI was conducted among WOAH poultry [commercial] table egg layer, 

pullet, and breeder bird farms in Delaware, Iowa, Maryland, Minnesota, Nebraska, Ohio, 

Pennsylvania, and Utah. This study was conducted by USDA–APHIS in collaboration with State 

partners, academia, and national poultry organizations. The goals of this study included identifying 

risk factors for HPAI and biosecurity challenges on WOAH poultry [commercial] table egg farms and 

refining biosecurity recommendations to support prevention of HPAI. This information will improve 

understanding of risk factors associated with HPAI on table egg farms in the U.S. and support 

science-based guidance on farm-level preventive measures. 

DATA COLLECTION 

Eligible case farms (infected farms) included those WOAH poultry [commercial] table egg layer, 

pullet, and breeder farms in the States listed above, with confirmed infection and reported onset of 

clinical signs from 22 February 2022 through 31 August 2022. A total of 22 farms met the inclusion 

criteria. While confirmed infections also occurred in several other States, these were not included 

due to resource constraints or lack of eligible control premises. Eligible control farms (uninfected 

farms) were any WOAH poultry [commercial] table egg layer, pullet, or breeder farms selected from 

the same States as case farms, using the USDA–APHIS–VS Emergency Management Response 

System. Randomized lists of 10 potential controls per case were shared with interviewers in each 

participating State, with a goal of enrolling up to two control farms per case farm. Potential controls 

were contacted by interviewers via phone or email to confirm eligibility and interest in participation. 

To be eligible, control farms needed to have 50,000 or more birds, as well as birds on-site for a 

minimum two-week window of risk within the State-specific high-risk timeframe. High-risk 

timeframes were determined according to reported onset of clinical signs for confirmed infections 

within the States. Interviewers were asked to match risk windows for cases and controls as closely 

as possible. 

Between 26 September 2022 and 28 December 2022, questionnaires were administered by Federal 

or State veterinary medical officers via telephone. The fillable pdf forms were then uploaded to a 

secure USDA–APHIS location. Interviewers in each State only had access to their State’s data, and all 

data was treated as confidential business information. Producer participation was voluntary. 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

DATA ENTRY AND MANAGEMENT 

Questionnaires were completed for 18 case farms and 22 control farms across 8 States (Figure 6). 

Survey data were entered into a SAS dataset using SAS version 9.4 (SAS Institute Inc., Cary, NC). 

Survey responses were validated by USDA–APHIS–VS National Animal Health Monitoring System 

(NAHMS) staff prior to analysis. Two primary approaches to multiple logistic regression were taken 

to glean the most information from this small dataset. The top findings are presented here. 

Figure 6. U.S. States with farms that participated in the 2022 HPAI H5N1 WOAH poultry [commercial] table egg 

case-control study. 

Additionally, using the results of whole genome sequencing from the NVSL, case farms that had 

virus sequences consistent with independent wild bird introduction of HPAI were further examined 

via univariate analyses. 

MULTIVARIABLE ANALYSIS 

The multivariable modeling results are summarized in Table 3 and Table 4 using two different 

modeling methods (using the best fit exact multiple logistic regression model and using Bayesian 

model averaging, which averages effects across all top models, respectfully). Findings from the 

modeling approaches are summarized below. 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Table 3. Estimated odds ratios, and their 95% confidence intervals, of an operation being positive for each of 

the variables included in the best fitting exact multiple logistic regression model. Also included are the pvalues for the tests that the effect size is non-zero. 

Variable Level Exact conditional test Odds ratio (95% 

p-value confidence interval) 

Flock size (number of birds on the Large (500,000) 0.59 2.6 (0.3 – 39.5) 

farm on the reference date) Small (<500,000) (referent) 

Farm in an existing control zone Yes 0.09 10.3 (0.8 – 377.0) 

on the reference date No (referent) 

Wild waterfowl or shorebirds in Yes 0.12 5.8 (0.7 – 79.4) 

closest crop field during the 14- No (referent) 

day reference period 

Gate to the farm entrance Yes 0.21 (referent) 

present No 3.8 (0.6 – 31.5) 

Personnel assigned to specific 

barns (dedicated barn personnel) 

Yes 

No 

0.34 (referent) 

6.2 (0.3 – 427.5) 

Table 4. Estimated odds ratios, and their 95% confidence intervals, of an operation being positive for each of 

the variables included in Bayesian model averaging. Also included are the estimated probabilities that the 

effect size is non-zero. 

Variable Probability the variable effect Odds ratio (95% confidence 

size is non-zero interval) 

Control zone 0.55 10.3 (1.1 – 100.5) 

No farm entrance gate 0.53 7.0 (1.1 – 43.7) 

Waterfowl presence 0.40 6.2 (1.1 – 39.6) 

Wild bird access to feed 0.25 5.0 (0.8 – 30.8) 

Flock size 0.22 5.9 (0.8 – 44.3) 

Offsite disposal 0.17 4.1 (0.7 – 25.5) 

No specific barn personnel 0.14 6.4 (0.4 – 97.1) 

At least some rodent problems 0.11 3.1 (0.6 – 15.3) 

Change of clothing not always required 0.10 4.5 (0.4 – 48.4) 

for workers 

Sharing company trucks/trailers 0.07 3.1 (0.4 – 23.5) 

Mowing less than 4 times/month 0.07 2.8 (0.4 – 18.6) 

Lower level of vehicle washing 0.07 2.7 (0.4 – 20.0) 

The most significant farm-level risk factor for HPAI on WOAH poultry [commercial] table egg farms 

was being located within an existing control zone. Farms that are located near an infected farm 

must be particularly diligent about biosecurity-related practices to protect flock health. Study 

findings confirm the need for both biosecurity and surveillance on poultry farms near an infected 

farm, to prevent infection and ensure rapid detection, whether the virus is likely spreading by wild 

birds or laterally between farms. 

Sightings of wild waterfowl or shorebirds were also associated with increased risk. While this result 

may be due in part to recall bias by producers on case farms, producers seeking to decrease risk for 

HPAI may wish to work with a wildlife management specialist to develop a wild bird management 

plan. Having feed or feed ingredients accessible to wild birds was also a risk factor, with 50 percent 

of case farms and only 27 percent of control farms reporting this access. In addition, although not 

statistically significant, only 40 percent of farms that had a protocol to clean spilled feed 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

immediately were classified as cases, while 60 percent of farms that had no protocol listed or a 

protocol to clean spilled feed less frequently were classified as cases. This further supports the need 

to include regular inspection of feed housing and prompt cleanup of feed spills in an overall flock 

management and wild bird management plan. 

The presence of a farm gate was found to be protective. Gates were much more commonly reported 

on control operations than on case operations (64 percent vs. 22 percent). Having a gate may be a 

proxy variable for other biosecurity practices and could even be associated with a highly proactive 

approach to biosecurity, i.e., gates improve control of traffic onto farms and may increase the 

likelihood that visitors will see posted signage and follow requested biosecurity procedures. 

Workers assigned to specific barns was found to be protective as movement of employees between 

barns is a known biosecurity risk. Having sufficient time and personnel can affect the degree to 

which workers are able to carry out good biosecurity practices. Flock size was non-significantly 

associated with increased risk, with larger operations tending to be more at risk than smaller 

operations in terms of number of birds on the operation. This may be a finding associated with 

selection bias because smaller control producers may have been more likely to participate in the 

study. 

A structural windbreak, such as a hill, was one of the factors univariately associated with decreased 

risk of wild bird introduction of HPAI at p ≤ 0.20; 0 percent of case farms and 30 percent of control 

farms reported having an on-farm structural windbreak. Reducing pooling of water around the farm 

environment is important in minimizing areas around the farm where wild birds may congregate and 

having a drainage ditch visible or within 350 yards of the farm was a risk factor; 64 percent of case 

farms had this feature, while 35 percent of control farms did. Having seen wild waterfowl or 

shorebirds in the closest field during the reference period was also a risk factor; 36 percent of case 

farms reported having seen wild waterfowl or shorebirds in the closest field during this timeframe, 

while only 5 percent of control farms did. A higher percentage of case farms reported having any 

rodent problem, with 73 percent compared to 40 percent of control farms. A higher percentage of 

case farms also reported wild bird access to feed or feed ingredients at least sometimes, with 73 

percent compared to 30 percent of control farms. Feed accessible to wild birds could act as a 

congregation point for wild birds on the farm and could increase risk of exposure to virus shed by 

affected wild birds. Cleaning up feed spills immediately was more common among control farms, 

with 80 percent compared to 50 percent of case farms. 

CONCLUSIONS AND NEXT STEPS 

This study compared management and biosecurity factors on case and control WOAH poultry 

[commercial] table egg farms in the U.S. during the 2022 HPAI H5N1 outbreak. Information on risk 

factors for infection has become increasingly important as this outbreak continues into 2023 and as 

additional infections in domestic poultry flocks, wild birds, and wildlife species are detected. Study 

results identified key risk factors associated with HPAI infection on farms and provided information 

that can be directly applied to support science-based updates to prevention and control 

recommendations to safeguard table egg farms in the U.S. 

A full description of this study, including methods and results, will be available in an open access 

peer-reviewed publication. 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Two additional topics were included in the case-control questionnaire but were not reported here. 

One section of the questionnaire related to barn-level factors on case and control farms. These data 

will be analyzed and reported separately. The questionnaire also included challenge-level questions 

asking for producers’ opinions on the level of challenge of certain topics, including biosecurity-, 

personnel-, and equipment-related issues. 

B. Turkey Case Control Study 

BACKGROUND 

WOAH poultry [commercial] turkey farms comprised the highest percentage of affected WOAH 

poultry [commercial] farms in the 2022–2023 HPAI outbreak in the U.S.; over 70 percent of all 

affected WOAH poultry [commercial] farms in the U.S. in 2022 were turkey farms. Wild bird 

introductions were identified as the primary mechanism of spread in this outbreak. In comparison, 

the 2015 outbreak was heavily influenced by lateral transmission of virus between farms. Several 

studies conducted during the 2015 HPAI outbreak explored potential risk factors for transmission of 

virus between farms (e.g., Dargatz et al, 2016; Garber et al., 2016; Wells et al., 2017). The 

differences in spread mechanism, as well as the larger geographic scope of the 2022–2023 outbreak 

as compared to the 2015 outbreak, necessitated further examination into transmission risk and 

biosecurity practices on turkey farms. 

At the request of and with support from State and national poultry organizations, USDA–APHIS 

conducted a case control study among WOAH poultry [commercial] meat turkey operations to 

investigate potential risk factors for introduction of HPAI virus onto farms. The objectives of the 

study included: 1) identify risk factors for infection with HPAI; 2) identify biosecurity challenges on 

turkey farms; 3) refine biosecurity recommendations to support prevention of infection on farms; 

and 4) identify priority areas for investment in biosecurity measures to reduce the risk of HPAI 

infection. 

DATA COLLECTION 

WOAH poultry [commercial] turkey farms that raised meat turkeys were eligible to participate in the 

study, whereas WOAH poultry [commercial] turkey breeder farms and WOAH poultry [backyard] 

farms with turkeys were excluded. Case farms were defined as farms that were confirmed to be 

positive for HPAI H5N1 by the NVSL between January 2022 and October 2022. Control farms were 

defined as farms that did not have HPAI in the same time period and were in the same State as case 

farms. Contact information for case and control farms was obtained from the USDA–APHIS–VS 

Emergency Management Response System, Thomson Reuters® CLEAR software, State databases 

where available, and poultry company representatives. At the start of the study, there were 161 

HPAI-affected WOAH poultry [commercial] meat turkey farms in 13 States. A total of 153 case farms 

from 13 States were contacted for participation, and 8 case farms were excluded due to a lack of 

contact information availability within the study timelines. 

A 24-page questionnaire (Appendix C: Commercial Turkey Case Control Survey) was administered to 

farm managers or supervisors on each participating farm via telephone by National Agricultural 

Statistics Service (NASS) enumerators, USDA–APHIS epidemiologists, or by mail. The questions 

focused on farm characteristics, wild birds, wildlife, biosecurity, personnel, visitors, vehicles and 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

equipment, and management practices for the 14 days prior to detection of infection on a case farm 

and a comparable 14-day reference period on control farms. Some questions asked about practices 

for the entire farm, and some asked about practices for a “selected barn.” The selected barn on case 

farms was the first barn on the farm to be confirmed HPAI positive, and for control farms, 

respondents were asked to identify a single barn at random to be designated as the selected barn. 

Data collection took place between 7 November 2022 and 27 February 2023. 

STATISTICAL ANALYSIS 

Survey responses were validated for error detection prior to analysis with SAS software. Data were 

analyzed to identify statistical associations between infected status (case vs. control) and farm or 

selected barn characteristics, such as management practices. The percentages of case and control 

farms having each characteristic were calculated. Univariate analyses were performed to identify 

variables potentially associated with the presence of HPAI. Variables with p ≤ 0.20 that were also

biologically plausible for risk of HPAI infection were considered for entry into candidate 

multivariable models. Multivariable logistic regression models were fit using forward, backward, and 

stepwise selection procedures. 

Case farms were subset by likely route of virus introduction (common source/lateral transmission or 

independent wild bird introduction) using the results of whole genome sequencing from NVSL. 

Subsets of farms that had either common source/lateral transmission or independent wild bird 

introduction were evaluated via univariate analyses, while a multivariable model was only created 

for wild bird introduction due to the low number of cases associated with common source/lateral 

transmission exposure between farms. 

MULTIVARIABLE ANALYSIS 

Questionnaires were completed for 67 case farms and 61 control farms across 12 States. One case 

and one control questionnaire were excluded because the farms had only breeder turkeys on-site 

during the 14-day reference period. One case farm completed both a case and a control 

questionnaire and the control questionnaire was subsequently excluded from this analysis. After 

excluding the farms without meat turkeys and adjusting for case-control status, 66 case farms and 

59 control farms across 12 States completed questionnaires (Figure 7). The sample included 30 

company farms, 50 contract farms (including lessees), and 44 independent farms; 1 farm had a 

missing response for this question. 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Figure 7. U.S. States with farms that participated in the 2022 HPAI H5N1 WOAH poultry [commercial] meat 

turkey case-control study. 

Seven variables remained in the final multivariable model (Table 5). Farms within an existing control 

zone had increased odds of being a case (odds ratio [OR] = 3.68, 95% confidence interval [CI] = 1.06– 

12.74). Other factors associated with increased odds of H5N1 HPAI infection included having both 

brooder and grower turkey production on the farm (OR = 7.35, CI = 2.51–21.54) and having toms as 

the sex market type on the farm (OR = 6.86, CI = 1.83–25.79). Seeing wild waterfowl or shorebirds in 

the closest field was also associated with increased odds of infection (OR = 6.02, CI = 1.83–19.78). 

The use of rendering for dead bird disposal during the 14-day reference period was associated with 

increased odds of infection (OR = 8.26, CI = 2.25–30.34). Factors found to have a protective effect 

included workers entering the selected barn using a shower during the 14-day reference period at 

least some of the time (OR = 0.29, CI = 0.09–0.98) and having a restroom facility available to crews 

who visit the farm (OR = 0.32, CI = 0.10–1.05). 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Table 5. Results of multivariable logistic regression analysis of factors associated with HPAI H5N1 infection on 

U.S. WOAH poultry [commercial] meat turkey farms. 

Characteristic % Case farms % Control farms Odds ratio (95% CI) p-value 

In an existing control zone 31.8 11.9 3.68 (1.06 – 12.74) 0.04 

Both brooder and grower stages 51.5 27.1 7.35 (2.51 – 21.54) <0.01 

on farm 

Sex: toms 86.4 67.8 6.86 (1.83 – 25.79) <0.01 

Waterfowl/shorebirds seen in 30.3 11.9 6.02 (1.83 – 19.78) <0.01 

closest field 

Worker biosecurity includes 10.6 27.1 0.29 (0.09 – 0.98) 0.05 

shower before entering barnA 

Restroom facility available to 45.5 69.5 0.32 (0.10 – 1.05)

B 0.05 

crews visiting farm 

Render dead birds 30.3 13.6 8.26 (2.25 – 30.34) <0.01 A Workers always, most of the time, or sometimes used the practice before entering the barn vs. never or not available. 

This question was asked specifically for the selected barn, and for the 14-day reference period. B Odds ratio is for comparison between always/sometimes available vs. never available. 

A multivariate model based on data from the subset of farms linked to wild bird introductions was 

similar to the risk factors identified from the farm-level model described above in Table 5, other 

than the control zone becoming non-significant (data not shown). 

CONCLUSIONS AND NEXT STEPS 

This study compared management and biosecurity factors on case and control meat turkey farms in 

the U.S. during the HPAI H5N1 outbreak in 2022–2023. Knowledge of risk factors for infection has 

become increasingly important as this outbreak continues into 2023 and as additional infections in 

domestic poultry flocks, wild birds, and wildlife species are detected. Study results identified key risk 

factors associated with HPAI infection on farms and provided information that can be directly 

applied to support science-based updates to prevention and control recommendations to safeguard 

turkey farms in the U.S. 

A full description of this study, including methods and results, will be available in a peer-reviewed 

publication. 

Future work may help further improve our understanding of the complex epidemiology of avian 

influenza transmission between wild birds and domestic poultry. Two additional topics were 

included in the case control questionnaire but were not reported here. One section of the 

questionnaire was related to biosecurity investments, including questions regarding ongoing 

biosecurity expenses and permanent and temporary improvements made since 2015 that impact 

farm biosecurity. These data will be analyzed and reported separately to identify priority areas for 

investment in biosecurity measures to reduce risk for HPAI. The questionnaire also included 

challenge-level questions asking for producers’ opinions on the level of challenge of certain topics, 

including biosecurity-, personnel-, and equipment-related issues. Finally, weather conditions and 

patterns related to avian influenza virus transmission have been examined previously and could 

have played a role in the outbreak in 2022–2023 (Chen et al., 2022; Liu et al., 2007; Si et al., 2013). 

Future work could expand upon the case control study presented here to incorporate weather 

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variables, such as temperature, relative humidity, precipitation, and wind speed in the time 

preceding detection to investigate the role of weather on risk of HPAI infection. 

C. Turkey Case-Control Study Economic Analysis 

PRELIMINARY RESULTS 

Initial results from the turkey case-control study show that there is heterogeneity between case and 

control farms in on-farm biosecurity and investments. Comparing mean values of data collected for 

control and case farms, we find that case farms were slightly larger, having a mean barn count of 

5.24, compared to 4.47 for control farms (statistically significant difference in means at p < 0.05). 

Control farms had statistically significant (p < 0.01) higher monthly biosecurity costs than case farms, 

$1,572 and $950, respectively. Control farms also spent more on temporary biosecurity measures 

($27,657 vs. $21,159; p < 0.01), such as gates, parking areas, temporary wild bird migration, 

temporary air intake inlet covers, or temporary vehicle wash stations. 

Logistic regression analyses show that there are heterogenous factors driving investments in 

biosecurity. National Poultry Improvement Plan (NPIP) participation increased the likelihood of 

investing in additional temporary biosecurity measures by 26.9 percent (p < 0.10). Dual sex farms 

were 0.2 percent more likely (p < 0.10) to spend more each month on biosecurity costs than single 

sex farms. This may be related to added precautions for birds, or the type of biosecurity system that 

requires more monthly outlays. Surprisingly, dual sex farms were 48.6 percent less likely (p < 0.01) 

to have invested in temporary biosecurity over the previous two years. This may reflect a more 

modernized infrastructure or an inclination for permanent investments over temporary for this 

production type. 

Farms that had permanently invested in improvements or renovations in the last year were less 

likely to have plans for future permanent investments. For example, a farmer who invested in a 

room that separates the “outside area” from the “inside area,” such as a Dutch entrance, was 

estimated to be 42.7 percent less likely to have permanent biosecurity investment plans. This may 

imply that those making the investment in the prior two years may have no economically feasible 

investments left to make. Importantly, case farms were 87.7 percent (p < 0.001) more likely to have 

plans to make permanent changes to biosecurity. This could signal ongoing and continued 

improvements in biosecurity to help mitigate HPAI incursions. 

The results presented here are preliminary. Analysis of the biosecurity investment data collected as 

part of the turkey case-control study is ongoing. Final results will be presented in a future report and 

in peer-reviewed publication. 

D. Turkey and Table Egg Study Weather Analysis 

BACKGROUND 

During the 2022–2023 HPAI outbreak in the U.S., several industry members expressed an interest in 

the role of weather in HPAI infections. Previous research has investigated the effects of 

temperature, humidity, and other weather variables on risk of avian influenza transmission (e.g., 

Chen et al. 2022; Liu et. al. 2018; Si et al., 2013). 

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USDA–APHIS is conducting a case-crossover study to examine associations between weather 

variables, such as wind speed, relative humidity, precipitation, and temperature, and HPAI infection 

on WOAH poultry [commercial] farms during the 2022 HPAI outbreak. Preliminary results are 

presented in this report, and this report only covers farms that were infected during 2022. 

DATA COLLECTION AND STATISTICAL ANALYSIS 

For this study, we included all WOAH poultry [commercial] turkey and table egg farms that were 

infected with HPAI in 2022, based on Emergency Management Response System (EMRS) data. This 

included turkey breeder, turkey meat production, layer breeder, layer pullet, and table egg layer 

farms. Each HPAI-affected farm served as its own control in a case-crossover study design. The 

hazard period was defined as the two weeks before onset of HPAI, and the control period was the 

two weeks before the hazard period (Figure 8). The hazard period was selected based on results 

from time of introduction analysis presented in this report. The control period was selected to be 

the same duration and close in time to the hazard period. 

Figure 8. Definition of hazard and control periods used in the WOAH poultry [commercial] turkey and table 

egg study weather analyses. 

Weather data for the hazard and control periods was obtained from gridMET (2023), a database 

containing daily weather information in 4 km2 grids across the U.S. Weather variables were 

averaged for each 14-day period of interest, and weather was compared between the hazard and 

control periods using conditional logistic regression models, which are appropriate for matched 

case-control data. The following weather variables were evaluated for a univariate association with 

HPAI infection risk on-farm: daily maximum temperature, daily minimum temperature, daily 

precipitation, daily average wind velocity, daily maximum relative humidity, daily minimum relative 

humidity, daily specific humidity, and downward shortwave radiation. 

PRELIMINARY RESULTS 

A total of 218 HPAI events on turkey farms and 37 HPAI events on layer farms were included in the 

analysis. The univariate analysis for turkey farms showed that increases in precipitation, minimum 

temperature, and wind speed were associated with increased risk of HPAI (Table 6). The univariate 

analysis for layer farms showed that increases in precipitation were associated with increased risk of 

HPAI ( 

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Table 7). 

Table 6. Results of univariate conditional logistic regression analysis of weather factors associated with HPAI 

H5N1 infection on U.S. WOAH poultry [commercial] turkey farms. 

Variable (14-day average) Median Hazard Median Control Odds ratio p-value 

Period Period (95% CI) 

Precipitation (mm) 1.43 0.78 1.28 (1.08 – 1.52) 0.004 

Minimum temperature -2.87 -3.68 1.08 (1.02 – 1.14) 0.006 

(

oC) 

Average wind speed (m/s) 5.10 4.47 4.25 (2.77 – 6.52) <0.001 

Table 7. Results of univariate conditional logistic regression analysis of weather factors associated with HPAI 

H5N1 infection on U.S. WOAH poultry [commercial] layer farms. 

Variable (14-day average) Median Hazard Median Control Odds ratio p-value 

Period Period (95% CI) 

Precipitation (mm) 1.44 0.84 1.52 (1.02 – 2.25) 0.038 

Most HPAI infections on turkey farms occurred in the spring. The higher HPAI risk with increasing 

temperature may not be a direct effect from temperature; instead, it may be an indirect effect from 

increasing wild bird activity as temperature increases in the spring. The results presented here are 

preliminary and should be interpreted cautiously since weather variables often have complex 

interactions. Multivariable modeling is needed before drawing final conclusions about associations 

between weather and HPAI risk. 

CONCLUSIONS AND NEXT STEPS 

Weather conditions, including wind, precipitation, and temperature may play a role in HPAI 

infection on WOAH poultry [commercial] farms. The next step for this study is to assess weather 

variables collectively using multivariable logistic regression modeling. Since many weather variables 

are related, multivariable modeling will allow the best understanding of how weather affects HPAI 

risk. 

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ESTIMATING THE TIME OF H5N1 HPAI INTRODUCTION INTO WOAH POULTRY 

[COMMERCIAL] FLOCKS USING DIAGNOSTIC TEST RESULTS AND PRODUCTION DATA 

A. Summary 

Determining the time of HPAI virus introduction in a flock is an important part of outbreak investigations. By 

narrowing the time window of possible virus introduction, we can better identify the potential transmission 

routes and enhance our understanding of the pattern of disease spread. In collaboration with researchers at 

the University of Minnesota, time of introduction (TOI) analysis was conducted on a subset of premises at 

the request of field responders and was dependent on the willingness of producers to provide the necessary 

data. Additionally, premises initially thought to be involved with lateral spread clusters were prioritized. 

Although most premises have more than one house of birds, TOI analysis was only performed on the house 

speculated to be the index case for the premises. Data utilized in the analysis included diagnostic testing, 

daily mortality, and water consumption data (where applicable). A total of 53 WOAH poultry [commercial] 

premises were analyzed, including 37 WOAH poultry [commercial] meat turkey, 4 broiler chicken, 8 table 

egg layer, 1 table egg layer pullet, 3 duck breeder, and 1 duck meat bird flocks. Detailed modeling 

methodology can be found in Appendix E: Time of Introduction Modeling Methods. 

B. Results 

The analyzed premises were grouped into anonymized State and phylogenetic clusters and results are 

presented by a cluster-specific, relative timeline (i.e., Day 1 for each cluster is a different calendar date than 

Day 1 for the other clusters; Figure 9). For each premises analyzed, a most likely day of introduction was 

estimated, as well as a 95 percent credibility interval, which represents a window of possible virus 

introduction for each premises. The day of presumptive diagnosis is also noted in (Figure 9) to provide an 

indication of the period of likely infectiousness for each premises. The source of introduction, also indicated 

in Figure 9, is based on phylogenetic analysis (see Phylogenetic Analysis and Diagnostics section for details) 

that is supportive of either independent wild bird introduction (IWBI) or common source/lateral spread (CS 

LT). Phylogenetic evidence is valuable in identifying and supporting potential sources of introduction but 

cannot be considered definitive proof and must be evaluated in conjunction with available epidemiological 

data. A few premises were classified as independent wild bird introduction with genotypic similarities 

(IWBI*), which means viruses isolated from these premises were either phylogenetically similar to those at 

other premises but had no plausible epidemiological links or were genetically similar to another premises’ 

virus but had more viral sequence mutations than those used to define CS LT cases. Among the premises 

included in this analysis, the phylogenetic data suggested 17 of the analyzed premises were IWBI, 6 premises 

were IWBI*, and 30 were CS LT. One premises included in this analysis was unable to be sequenced. 

Each cluster presents a unique pattern, that in combination with phylogenetic evidence, can be suggestive 

of the timing and routes of introduction to help narrow the focus of epidemiologic investigations. 

State A had four premises analyzed as part of a regional cluster of six premises. Phylogenetic analysis 

suggested three of these premises were the result of an IWBI. One of the IWBI premises was 

phylogenetically linked to three premises thought to be infected via a common source or lateral spread. 

Time of introduction analysis was only performed on one of the linked premises and the estimated window 

of likely virus introduction occurred after the detection of the initially infected premises. One of the 

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premises not analyzed was detected in between these two premises, which suggests it may have played a 

role in the transmission between the cluster of farms; however, field investigations did not identify direct 

epidemiological links between the four phylogenetically-linked premises. 

The analyzed premises in State B and State C are geographically related and part of a cluster of seven 

premises detected in a one-month period initially speculated to be a phylogenetic cluster. Field investigators 

only identified epidemiological links between two premises in State B, and both premises belonged to the 

same corporate producer. A notable observation in these clusters is the wide time range of possible 

introduction and the time to detection for the broiler premises in State B. Time of introduction analysis 

relies heavily on baseline mortality data. Prior to detection, this premises had an increase in mortality 

associated with another pathogen that resolved prior to the rapid increase in HPAI-associated mortality. In 

addition, diagnostic samples were collected, and the premises was quarantined on a Friday, but the samples 

were not analyzed until the following Monday, delaying the initial diagnosis. 

The two analyzed premises in State D were in a phylogenetic cluster of seven infected premises attributed to 

common source or lateral spread transmission. While the definitive causes of spread between all premises 

were not determined, field investigation identified company affiliations, shared farm personnel, equipment, 

vehicles, and contracted rendering services as potential routes of transmission. 

State E had several phylogenetic clusters during the outbreak. Time of introduction analysis was only 

performed on a subset of these premises due to data and resource availability. Several of the premises 

analyzed were initially thought to be a part of lateral spread clusters based on their geographic proximity to 

other infected premises. For example, two turkey meat bird premises in the independent cluster were 

initially assumed to be associated with the premises in cluster 4 due to their relative locations; however, 

genetic sequencing indicated these premises were not linked phylogenetically. Rather, the premises in 

cluster 4 was linked to a separate premises that was not analyzed. Results for seven out of nine premises in 

cluster 5 are shown in Figure 9. Although two premises were not analyzed, the windows of introduction for 

the premises potentially infected by a common source or lateral spread are after the day of presumptive 

diagnosis for the clusters index case. Analytical epidemiologists investigated the potential for windborne 

transmission during the depopulation and disposal of the index premises, based on the shared geographic 

relationship between index premises and the cluster premises subsequently detected. 

Results are presented for 10 out of 16 premises in a phylogenetic cluster in State F. Time of introduction 

results for the WOAH poultry [commercial] duck premises should be cautiously interpreted due to limited 

information to inform modeling priors and the unique structure of WOAH poultry [commercial] duck 

production facilities. Potential sources of lateral spread within this cluster included employees with common 

living arrangements, egg movements, and shared company ownership. 

State G is the last analyzed State with phylogenetic clusters. This State had 2 temporal clusters of HPAI 

cases—originally a cluster of 3 premises, subsequently followed by a cluster of 15 premises. In the first 

cluster, a rendering truck was speculated to be involved in lateral transmission; however, a unique genotypic 

mutation assumed to occur in a wild bird suggested the third infected premises was the result of a separate 

wild bird introduction. Given the relative proximity of these premises to each other, it is plausible that the 

three barns were infected from a common wild bird source. In the second cluster, premovement tests failed 

to capture an infected premises that led to the infection of three other premises; definitive sources of 

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spread for the remaining 12 premises in the cluster were not identified, though potential sources included 

company affiliation, spatial proximity, feed delivery, and the movement of people. 

Figure 9. Relative timeline for time of introduction analysis by State, phylogenetic cluster, production type, and likely 

source of introduction. 

In addition to contributing to epidemiological investigations, time of introduction analysis can provide 

insight into how rapidly cases were detected following virus introduction and to within-house virus-spread 

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dynamics. To assess the timeline of case detection, we examined the time to first positive sample (TFPS), 

which was the time difference between the estimated time of flock exposure and when the first rRT-PCR 

positive samples were collected. The observed differences in TFPS among the production types are seen in 

Figure 10. Table egg layers or pullet premises had the shortest TFPS, with a range of two to six days. Broiler 

production premises had the longest TFPS, with a range of 8 to 20 days. Turkey meat bird and duck premises 

were in between with a range of 4 to 11 days from the most likely day of virus exposure to disease 

detection. 

The shorter TFPS for table egg layers may be because seven out of nine table egg layer premises included in 

the analysis were under active surveillance as part of Control Area or Surveillance Zone protocols. These 

premises were frequently submitting diagnostic tests for permitted egg movements. Overall, when premises 

are grouped by reason for testing, the estimated median TFPS was six days for premises under ongoing 

surveillance testing (e.g., testing within a Control Area or Surveillance Zone or for movement permits), and 

eight days when testing was requested based on observing HPAI clinical signs in the flock. When grouped by 

the likely source of introduction, the estimated median TFPS was six days for common source or lateral 

spread introductions and eight days for independent wild bird introductions. This pattern held constant 

across production types. A possible explanation for the earlier detection of common source or lateral spread 

infections is the local area surveillance activities that occur after a detection. 

Figure 10. Time from estimated HPAI introduction to detection by production type and likely source of introduction. 

The estimated adequate contact rate, or transmission parameter, is the number of contacts per day a bird 

has with other birds that would be sufficient to result in infection. This is the parameter that determines the 

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rate of virus spread within the flock. The mean of the most likely value for the adequate contact rate from 

all premises was 4.9 contacts per day (range 0.5–18.7 contacts per day; Figure 11). Contact rates were 

similar across all production types, except for broiler production premises. The mean contact rate was 5.0 

contacts per day (range 0.5–14.1) for turkey premises, 5.8 contacts per day (range 1.1–18.7) for table egg 

layer and pullet premises, 5.3 contacts per day (range 1.1–8.7) for duck premises, and 1.7 contacts per day 

(range 0.6–2.7) for broiler premises. The reason for the difference between broiler production premises and 

the other production types is unknown but may be a combination of factors related to species, housing, and 

other management practices. For example, turkey meat bird and broiler production premises are both floorraised production types, where birds have the opportunity to interact with any other bird in the house; 

however, past studies have shown turkeys to be more susceptible to avian influenza viruses than chickens, 

which may result in a higher rate of spread in turkey houses (Pillai, Pantin-Jackwood, Yassine, Saif, & Lee, 

2010). The difference between broilers and table egg layers may be related to differences in housing type, 

ventilation, foot traffic, or other production practices that could increase the rate of spread in table egg 

layer houses compared to broilers. When grouped by the source of introduction, the estimated mean 

contact rate was 4.8 for CS LT and 5.1 for IWBI. 

Figure 11. Estimated adequate contact rate by production type and likely source of introduction, estimated by time of 

introduction analysis. 

The following is a similar breakdown by production type for the estimated basic reproduction number (R0; 

Figure 12). The overall mean R0 value was 13.5 (range 2–62). For turkeys, the mean R0 was 16.3 (range 3– 

47). For table egg layer and pullet premises, the mean R0 was 11.9 (range 2–37). For the broilers, the mean 

R0 was 5.6 (range 2.4–8). For ducks, the mean R0 was 36.75 (range 9–62). The basic reproduction number is 

a function of the rate of transmission and the duration of infectiousness; therefore, the difference in R0 

between turkeys and table egg layers that was not observed in their contact rates could be due to 

differences in the duration of infectiousness. As mentioned previously in relation to TFPS, the difference in 

duration of infectiousness may be related to faster detection in table egg layers than turkeys because of a 

greater intensity of active surveillance and/or premovement testing applied to the table egg layers in this 

analysis. The H5N1 virus responsible for these infections is particularly adapted to waterfowl and may 

explain why WOAH poultry [commercial] ducks had higher reproduction numbers. Grouped by source of 

introduction, the average basic reproduction number was 16.7 for CS LT and 15.8 for IWBI. 

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Figure 12. Basic reproduction number (R0) by production type and likely source of introduction, estimated by time of 

introduction analysis. 

C. Discussion 

Estimating the time of HPAI virus introduction provides a valuable piece of information for epidemiologic 

investigations and outbreak response. In this analysis, we estimated the time window for HPAI introduction 

and transmission parameters for 53 infected barns using diagnostic test results and production data. The 

analysis was used to narrow the time window of possible virus introduction to help identify routes of 

transmission. 

This work is dependent on information on the progression of disease mortality and clinical signs from 

production records and regular laboratory diagnostic testing. Access to different categories of detailed, high 

quality production data, such as daily mortality, egg production, and water consumption helps to provide 

more robust estimates of the time of introduction and reduce the uncertainty. For example, the estimated 

time of introduction 95 percent credible interval was narrower where both daily mortality and water 

consumption data were incorporated into the analysis. Conversely, the estimated intervals for time of 

introduction were wider for premises without elevated mortality and with fewer days of diagnostic testing. 

This work also highlights the value of closely monitoring mortality, water consumption, and egg production 

to quickly identify disease issues in the flock. These factors may vary across flocks and between barns, so 

understanding the trends within each production setting is important. It should also be acknowledged that 

model results rely on input parameters from HPAI experimental studies and may vary as data from newer 

studies are considered; however, preliminary sensitivity analysis suggests that time of introduction 

estimates are relatively robust, and changes are not anticipated to be substantial. 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

AVIAN INFLUENZA SURVEILLANCE IN WILD BIRDS 

A. Background 

Waterfowl are natural reservoir hosts for influenza A viruses (IAV; subtypes H1-H16), but not 

usually highly pathogenic avian influenza. Influenza A viruses in wild birds tend to circulate 

seasonally within migratory flyways, and subtype prevalence can wax/wane in multiyear cycles. 

Areas where birds from different flyways congregate provide opportunities for viruses to mix 

across flyways. 

Waterfowl migration in North America generally consists of north-south seasonal movements 

between breeding grounds and wintering areas. There are four major flyways in North America ( 

Figure 13). These flyways are broadly defined corridors where the migratory paths of many 

species of interest tend to converge and are associated with major topographical features in 

North America, which also tend to be aligned along a north-south axis. The four North American 

flyways have areas of overlap and convergence, particularly at the north and south ends. Flyway 

boundaries are defined administratively and are not biologically fixed or sharply defined. 

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Figure 13. Map depicting the four primary North American waterfowl flyways.7 

North American flyways represent the predominant pathways of migratory bird movements within broad 

geographic areas. Many migratory bird species use specific flyways during spring and fall; however, many 

species migrate across flyways. During migratory movement, wild birds have the potential of dispersing 

pathogens, such as IAV, across wide geographic distances. 

The first detection of Eurasian strain (EA) H5N1 HPAI in North America occurred in a great blackbacked gull in December 2021 in Newfoundland and Labrador, Canada. The bird was showing 

neurologic signs and was part of a large mortality event. The first subsequent detection of H5N1 

HPAI in the U.S. was reported in January 2022 in a dabbling duck from South Carolina. The bird 

was exhibiting no neurologic signs and was an apparently healthy bird collected during hunter 

harvest. 

B. Wild Bird Surveillance Program 

The U.S. National Surveillance Plan for Highly Pathogenic Avian Influenza in Wild Birds was 

developed to maximize our ability to detect IAV in wild waterfowl. Surveillance helps to 1) 

understand how IAV is distributed in the U.S.; 2) detect the spread of IAV to new areas of 

concern; and 3) monitor wild dabbling duck populations for introductions of novel viruses (e.g., 

Eurasian lineage H5 and H7). Targeted surveillance focuses on sampling apparently healthy 

dabbling duck species from areas with extensive mixing of wild bird populations and a history of 

IAV detection. 

Between 30 December 2021 and 31 March 2023, over 40,000 apparently healthy wild waterfowl 

were sampled and tested by rRT-PCR for IAV. Wild bird surveillance testing follows the NAHLN 

testing algorithm––samples are first tested by a Type A-specific test (IAV-M) and further tested 

by the H5/H7 subtype tests in samples where viral RNA is detected. H5 and H7 positive samples 

are forwarded to NVSL for confirmatory testing. The number of H5N1 lineage virus detections is 

based on viruses confirmed at NVSL from H5N1 presumptive samples forwarded by NAHLN 

laboratories. Overall, targeted wild bird surveillance conducted by USDA–APHIS–WS has resulted 

in 2,264 detections of H5N1 HPAI lineage virus across all four administrative flyways (Table 8). 

Table 8. Number of H5N1 HPAI detections from apparently healthy wild birds sampled by USDA–APHIS–WS between 1 

June 2022 and 31 March 2023. 

Flyway # Birds Sampled # H5N1 HPAI Detections 

Atlantic 12,920 667 

Mississippi 10,569 584 

Central 5,899 443 

Pacific 10,717 570 

7 Ducks Unlimited Canada. (n.d.). Flyways of North America [Map]. Retrieved June 21, 2022, from 

https://www.multivu.com/players/English/7804651-ducks-unlimited-migration 

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Total 40,105 2,264 

C. Morbidity/Mortality Sampling 

The investigation of morbidity/mortality events is another important strategy for detection of HPAI in wild 

birds. During morbidity/mortality events, sick or dead birds may be submitted for testing and cause-of-death 

determination, and a subset of birds may be sampled for IAV testing. Investigations related to 

morbidity/mortality events are conducted regardless of the time of year or species involved, and 

morbidity/mortality events may involve one bird or hundreds of birds (although a small subset of birds are 

typically sampled at large-scale die offs). Morbidity/mortality samples are collected by a wide variety of 

entities, including but not limited to USDA–APHIS–WS, State wildlife agencies, the U.S. Fish and Wildlife 

Service, USGS National Wildlife Health Center, and universities. 

Between 30 December 2021 and 31 March 2023, morbidity/mortality investigations resulted in 

3,639 detections of H5N1 HPAI lineage virus in sick or dead birds across all four Flyways: Atlantic 

– 1,033; Mississippi – 990; Central – 752; and Pacific – 864. Altogether, targeted surveillance 

samples collected by USDA–APHIS–WS and other agencies, and morbidity/mortality 

investigations of sick or dead birds during this time period have resulted in 6,086 detections of 

H5N1 HPAI lineage virus in over 130 wild bird species across 49 States, plus Washington, D.C. 

(Figure 14 and Table D1). 

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Figure 14. Number of H5N1 HPAI detections in wild bird species tested between 1 June 2022 and 31 March 2023. State 

totals include detections from both apparently healthy birds and sick/dead birds sampled as part of 

morbidity/mortality investigations. 

D. HPAI Detections in Mammals 

Although IAVs primarily affect poultry and wild birds, these viruses can occasionally be transmitted to 

mammals. A rising number of H5N1 HPAI cases have been reported in several terrestrial and aquatic 

mammalian animals across the U.S. (Figure 15). Infection may cause illness, including severe disease and 

death in some cases. As of 31 March 2023, there have been 154 H5N1 HPAI detections in at least 17 wild 

mammal species in 23 States since the start of the 2022 - 2023 HPAI outbreak. All the H5N1 HPAI detections 

in mammals have been from sick or dead animals. There is currently no nationwide active HPAI surveillance 

effort in apparently healthy wild mammals. 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Figure 15. Detections of HPAI in mammals as of 31 March 2023. 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

MODELING AVIAN INFLUENZA TRANSMISSION AT THE INTERFACE OF WILD BIRDS AND 

DOMESTIC POULTRY 

A. Background

With support from USDA–APHIS, collaborators from the United States Geological Survey (USGS) and the 

University of Maryland are currently modeling the risk of avian influenza virus transmission from wild 

waterfowl to domestic poultry across the contiguous U.S. The objectives of the study include the creation of 

fine scale spatio-temporal transmission risk estimates of spillover of virus from wild birds to domestic 

poultry for the contiguous U.S., and identification of factors influencing changes in relative risk of spillover 

across the landscape through time. 

B. Methods

MODELING FRAMEWORK

Our objective is to model variation in both the spatial and temporal risk of an avian influenza spillover 

event from wild reservoir species into domestic poultry operations. Spillover events are generally not 

reported in the U.S. for viruses of low-pathogenicity, and incursion of highly pathogenic viruses has 

historically been rare; therefore, little data have been available to predict the risk of spillover from wild 

birds to domestic poultry. 

The risk of a wild to domestic spillover event (hereafter, spillover event) can be modeled as the 

transmission risk (R) between wild birds and domestic poultry operations using the following equations: 

RR = WWii × PPrr

where Wi is the estimated number of infected waterfowl present at a given time and place and Pr is the 

number of poultry facilities in that location weighted by their risk of a spillover event occurring given 

facility type. This equation can be further broken down to: 

where As is the abundance of waterfowl of species s, Ps is the percentage of those waterfowl positive 

with avian influenza virus, Nt is the number of poultry operations of a given type t, and Rt is the relative 

risk associated with each operation type. 

Estimates of waterfowl abundance (As) were taken from the predicted relative abundance models 

generated for eBird Status & Trends (Fink et al., 2020). We included estimates for 30 common waterfowl 

species. The percentage of infected waterfowl (Ps) of each species at each weekly interval comes from a 

previous effort to model avian influenza prevalence in wild waterfowl (Kent et al., 2022), and the 

number and type of poultry operations (Nt) come from a previously developed model (Patyk et al., 

2020). Finally, as there is known variation in the relative risk of different farm types, we developed a 

relative risk scaler for each poultry operation type. 

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MODEL VALIDATION 

In general, these models are designed to estimate the risk of spillover of low-pathogenicity endemic 

viruses into domestic poultry operations, but validation data for such spillover events are generally not 

available in the U.S. We instead used data from the current U.S. HPAI outbreak for model validation. 

Model validation took place at the county level by summing predicted risk within each county for each 

weekly step. Inference on model validation was based on the area under the receiver operating 

characteristic curve (AUC) to understand the model’s ability to correctly identify counties that 

experienced a spillover event. This value was based on whether a county experienced a spillover event 

in each week and the rank-relative risk for that county during that week. 

C. Preliminary Results

In general, we see the predicted risk of spillover events shifting north and south with waterfowl migration, 

with the overall level of risk rising and falling with avian influenza prevalence, reaching its lowest levels in 

late spring and early summer. Additionally, we see some areas of particularly high poultry production that 

remain at an elevated risk year-round. Results from selected weeks can be viewed in Figure 16. 

Figure 16. Model-predicted risk of avian influenza spillover from wild waterfowl to domestic poultry across the 

contiguous United States during four selected weeks of the year. 

Data through January 2023 of the current outbreak were used to evaluate model performance. Outbreaks 

overwhelmingly occurred in counties with greater than average risk (Figure 17), and overall, the model 

appears to have performed well at predicting spillover events during the current HPAI outbreak. In counties 

with above-average risk, 244 spillover events occurred, while only 20 occurred in counties with a belowaverage risk. Only 5 five spillover events occurred in counties categorized as "low risk" by the interface 

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model, compared to 195 spillover events in "high-risk" counties. Model results are now available online for 

poultry owner use to better understand their own risk context.8 

Figure 17. Distribution of risk values across all counties (grey bars) for each week of the year in which spillover events 

occurred. Red lines indicate the risk level for counties that actually had spillover events. 

D. Next Steps 

The data presented here represent preliminary results, and models are still being finalized. Once models are 

finalized and validated, they will be published and results shared publicly for use by interested managers, 

policy makers, and researchers. 

It is important to note that these models are not meant to be static elements without the inclusion of new 

data. Concurrent with the finalization of these initial models, we are beginning a regression analysis on HPAI 

outbreak locations and associated covariates, ranging from production type to surrounding habitat features. 

Lessons learned from this analysis could then be integrated into future iterations of the interface models, 

further refining elements, such as the relative risk scaler based on poultry operation type. 

8 https://www.pwrc.usgs.gov/ai/ 

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ANALYSIS OF BIRDCAST AND E-BIRD MIGRATION DATA: IMPLICATIONS FOR DISEASE 

INTRODUCTION, SPREAD, AND PREVENTION 

A. Potential Use of BirdCast Data for Awareness to Enhance Prevention Measures 

As a prevention tool following initial detections of HPAI in wild birds in the U.S., BirdCast notes dates, times, 

and areas of more intense wild bird migration can be used to increase awareness of potential increased risk 

to poultry producers. The following 22 September 2022 22:10 ET BirdCast live bird migration map, with a 

height of 813.2 million of birds in flight in a point in time over a 24-hour period, depicts strong pink-orange 

to yellow-white colors indicating areas of more intense density of bird migration in all or parts of a State, 

including Wisconsin, Massachusetts, Michigan, eastern Minnesota, New Hampshire, Ohio, western 

Pennsylvania, and Tennessee, among others (Figure 18). 

Figure 18. BirdCast Live Bird Migration Map of 22 September 2022 at 22:10 ET. 

The NVSL presented phylogenetic analyses on 26 September 2022 and 5 October 2022 of samples collected 

from WOAH poultry [commercial] and WOAH poultry [backyard] premises from the aforementioned States. 

They identified all as most likely caused by independent wild bird introduction (IWBI) by looking at just one 

of the genotypes, H5N1 HPAI genotype B1.2, circulating since 4 April 2022, though increasing in prevalence 

in the samples in September 2022 (Figure 19). 

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0 

5 

10 

15 

20 

25 

30 

Apr-22 May-22 Jun-22 Jul-22 Aug-22 Sep-22 Oct-22 Nov-22 Dec-22 Jan-23 Feb-23 Mar-23 

IWBI B1.2 detections on Commercial and Backyard poultry premises 

IWBI Genotype B1.2 detections by Wild Bird Flyways by Analysis Date 

Highly Pathogenic Avian Influenza H5N1 clade 2.3.4.4b virus detections on Commercial and Backyard flocks by Flyway 

collected and sequenced between April 2022 and March 2023 

identified as Independent Wild Bird Introductions (IWBI) of Genotype B1.2 

Atlantic Central Mississippi 

Figure 19. H5N1 HPAI clade 2.3.4.4b virus of genotype B1.2 detections in WOAH poultry [commercial] and WOAH 

poultry [backyard] from April 2022 to March 2023 identified as IWBI. 

Notable differences between numbers of birds in flight from 15 July 2021 through 31 March 2022 and 15 

July 2022 through 31 March 2023 are likely explained by weather impacts, which may influence risk of HPAI 

exposure on WOAH poultry [commercial] premises. The increase in density of millions of birds in flight 

preceded increases in numbers of HPAI-positive wild birds and poultry premises, particularly in September 

and October 2022. Similarly, decreases in positive poultry premises followed observed decreases in 

BirdCast’s migration density, as tracked by millions of birds in flight per evening (Figure 20).

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Figure 20. Overlapping 15 July 2021 through 31 March 2022 and 15 July 2022 through 31 March 2023, BirdCast’s 

highest daily number of millions of birds in flight by day is shown over daily counts of H5 and H5N1 HPAI detections 

in wild birds, WOAH non-poultry, and WOAH poultry premises between 15 July 2022 and 31 March 2023. 

B. eBird Output of Relative Abundance of Migrating Birds

eBird outputs provide additional information on potential indicators of risk for HPAI transmission from 

specific wild bird species in flight and opportunities for prevention. Relative abundances recorded in the 

eBird dashboard are counts of individual birds of a given species detected by an expert. User skill, hourly 

weather conditions, specific for a given region, season, and species are considered to maximize detection 

rates. For each species, relative abundance is estimated for all 52 weeks of the year across a regular spatial 

grid with a density of one location per 2.96 km x 2.96 km. Estimates at each location and date are made 

based on the local habitat, elevation, and topography (Figure 21). 

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Figure 21. Maps pulled from eBird Status and Trends in the U.S.9 for the week of 21 September 2022, focused on the 

relative abundance of blue-winged teal, Canada goose, and mallard species. 

9 https://science.ebird.org/en/status-and-trends/species/wooduc/abundance-map-weekly?week=38 

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REFERENCES 

Animal and Plant Health Inspection Service. (2023). 2022-2023 Confirmations of Highly Pathogenic Avian 

Influenza in Commercial and Backyard Flocks. U.S. Department of Agriculture. 

https://www.aphis.usda.gov/aphis/ourfocus/animalhealth/animal-disease-information/avian/avianinfluenza/hpai-2022/2022-hpai-commercial-backyard-flocks 

Animal and Plant Health Inspection Service. (2023a). 2022-2023 Detections of Highly Pathogenic Avian 

Influenza in Mammals. U.S. Department of Agriculture. 

https://www.aphis.usda.gov/aphis/ourfocus/animalhealth/animal-disease-information/avian/avianinfluenza/hpai-2022/2022-hpai-mammals 

Animal and Plant Health Inspection Service. (2022). USDA Confirms Highly Pathogenic Avian Influenza in a 

Wild Bird in South Carolina. U.S. Department of Agriculture. 

https://www.aphis.usda.gov/aphis/newsroom/stakeholder-info/sa_by_date/sa-2022/hpai-sc 

Animal and Plant Health Inspection Service. (n.d.). Wild Bird Avian Influenza Surveillance USDA APHIS - data: 

July 2021 - Dec 2022. U.S. Department of Agriculture. https://www.aphis.usda.gov/aphis/maps/animalhealth/wild-bird-avian-flu-surveillance 

Chen, W., Zhang, X., Zhao, W., Yang, L., Wang, Z., & Bi, H. (2022). Environmental factors and spatiotemporal 

distribution characteristics of the global outbreaks of the highly pathogenic avian influenza H5N1. 

Environmental Science and Pollution Research. https://doi.org/10.1007/s11356-022-19016-1 

Climatology Lab. (n.d.). gridMET. Retrieved 2023, from https://www.climatologylab.org/gridmet.html 

Dargatz, D., Beam, A., Wainwright, S., & McCluskey, B. (2016). Case Series of Turkey Farms from the H5N2 

Highly Pathogenic Avian Influenza Outbreak in the United States During 2015. Avian Diseases, 60(2), 

467–472. https://doi.org/10.1637/11350-121715-reg 

Ducks Unlimited Canada. (n.d.). Flyways of North America [Map]. Retrieved June 21, 2022, from 

https://www.multivu.com/players/English/7804651-ducks-unlimited-migration/ 

Fink, D., Auer, T., Johnston, A., Ruiz-Gutierrez, V., Hochachka, W. M., & Kelling, S. (2020). Modeling avian full 

annual cycle distribution and population trends with citizen science data. Ecological Applications. 

https://doi.org/10.1002/eap.2056 

Garber, L., Bjork, K., Patyk, K., Rawdon, T., Antognoli, M., Delgado, A., Ahola, S., & McCluskey, B. (2016). 

Factors Associated with Highly Pathogenic Avian Influenza H5N2 Infection on Table-Egg Layer Farms in 

the Midwestern United States, 2015. Avian Diseases, 60(2), 460–466. https://doi.org/10.1637/11351-

121715-reg 

GISAID - gisaid.org. (n.d.). Gisaid.org. https://gisaid.org/ 

Freath, L., Brown, I., Banyard, A., Byrne, A., Pacey, A., Gale, P., & Perrin, L. (2022). Highly pathogenic avian 

influenza (HPAI) in the UK and Europe. UK Animal and Plant Health Agency. 

https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/10 

70246/Highly_pathogenic_avian_influenza__HPAI__in_the_UK_and_Europe__outbreak_update_23.pdf 

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Kent, C. M., Ramey, A. M., Ackerman, J. T., Bahl, J., Bevins, S. N., Bowman, A. S., Boyce, W. M., Cardona, C. J., 

Casazza, M. L., Cline, T., Susan, Hall, J. C., Hill, N. J., Ip, H. S., Krauss, S., Mullinax, J. M., Nolting, J. M., 

Plancarte, M., Poulson, R. L., & Runstadler, J. A. (2022). Spatiotemporal changes in influenza A virus 

prevalence among wild waterfowl inhabiting the continental United States throughout the annual cycle. 

12(1). https://doi.org/10.1038/s41598-022-17396-5 

Lesley, C. (2021). 5 ways 2020 changed the backyard chicken industry. The Poultry Site. 

https://www.thepoultrysite.com/articles/5-ways-2020-changed-the-backyard-chicken-industry 

Liu, T., Kang, M., Zhang, B., Xiao, J., Lin, H., Zhao, Y., Huang, Z., Wang, X., Zhang, Y., He, J., & Ma, W. (2018). 

Independent and interactive effects of ambient temperature and absolute humidity on the risks of avian 

influenza A(H7N9) infection in China. Science of the Total Environment, 619-620, 1358–1365. 

https://doi.org/10.1016/j.scitotenv.2017.11.226 

Patyk, K. A., McCool-Eye, M. J., South, D. D., Burdett, C. L., Maroney, S. A., Fox, A., Kuiper, G., & Magzamen, 

S. (2020). Modelling the domestic poultry population in the United States: A novel approach leveraging 

remote sensing and synthetic data methods. Geospatial Health, 15(2). 

https://doi.org/10.4081/gh.2020.913 

Si, Y., de Boer, W. F., & Gong, P. (2013). Different Environmental Drivers of Highly Pathogenic Avian Influenza 

H5N1 Outbreaks in Poultry and Wild Birds. PLoS ONE, 8(1), e53362. 

https://doi.org/10.1371/journal.pone.0053362 

WAHIS. (2023). Event 4191. World Organisation for Animal Health. https://wahis.woah.org/#/inevent/4191/dashboard 

Wells, S. P., Kromm, M., VanBeusekom, E. T., Sorley, E. J., Sundaram, M. E., VanderWaal, K., Bowers, J., 

Papinaho, P. A., Osterholm, M. T., & Bender, J. (2017). Epidemiologic Investigation of Highly Pathogenic 

H5N2 Avian Influenza Among Upper Midwest U.S. Turkey Farms, 2015. 61(2), 198–198. 

https://doi.org/10.1637/11543-112816-reg.1 

World Health Organization. (2022, December 21). Assessment of risk associated with the recent influenza 

A(H5N1) clade 2.3.4.4b viruses (Rapid Risk Assessment). 

https://www.who.int/publications/m/item/assessment-of-risk-associated-with-recent-influenzaa%28h5n1%29-clade-2.3.4.4b-viruses 

Youk, S., Torchetti, M.K., Lantz, K., Lenoch, J.B., Killian, M.L., Leyson, C., Bevins, S.N., Dilione, K.E., Ip, H.S., 

Stallknecht, D.E., Poulson, R.E., Suarez, D.L., Swayne, D.E., & Pantin-Jackwood, M.J. (2023). H5N1 highly 

pathogenic avian influenza clade 2.3.4.4b in wild and domestic birds: Introductions into the United States 

and reassortments, December 2021-April 2022. SSRN. http://dx.doi.org/10.2139/ssrn.4477349 

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ACKNOWLEDGMENTS 

We greatly appreciate the cooperation and support of the poultry industry, particularly the producers and 

farm owners for allowing access to their properties, providing biosecurity and production practice 

information, and their full cooperation with these investigations. 

We also appreciate the diligent efforts of State partners and USDA–APHIS–VS and USDA–APHIS–WS 

responders to collect epidemiologic data and their partnership on the resulting analyses. 

This report would not have been possible without the many researchers, epidemiologists, economists, 

laboratory staff, and data scientists who analyzed, drafted, and reviewed this report. We would like to 

extend our thanks to the National Veterinary Services Laboratory (NVSL), the Center for Informatics (CFI), 

Secure Poultry Supply (SPS, University of Minnesota), the Cornell Lab’s BirdCast staff (BirdCast), and State 

veterinary diagnostic laboratories. 

We’d like to convey our specific gratitude to the following individuals: 

- Dr. Jada Thompson (University of Arkansas) 

- Dr. Amos Ssematimba, Dr. Sasidhar Malladi, and Peter Bonney (SPS, University of Minnesota) 

- Dr. Adriaan Dokter and Dr. Andrew Farnsworth (BirdCast) 

- Dr. Mia Torchetti, Dr. Kris Lantz, Tod Stuber, Jessica Hicks, and Cameron Norris (NVSL) 

- Dr. Philip Riggs, Dr. Jared Luxton, and Dr. Carolann Knutson (CFI) 

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APPENDIX A: DETAILED OUTBREAK OVERVIEW BY FLYWAY 

MISSISSIPPI FLYWAY February – March 2022 

On 7 February 2022, one WOAH poultry [commercial] turkey meat bird operation in Dubois County, 

Indiana, submitted diagnostic test samples to the Indiana Animal Disease Diagnostic Laboratory (a 

member of the NAHLN) after observing signs of lethargy, increased mortality, and decreased water 

consumption in one tom turkey production house. The samples tested non-negative for H5 and were 

forwarded to the NVSL. On 8 February 2022, the NVSL received samples from the affected premises and 

confirmed clade 2.3.4.4b H5N1 HPAI. 

Continuing in the Mississippi Flyway, the next States affected were Kentucky and Virginia. On 11 

February 2022, one WOAH poultry [commercial] broiler production operation in Fulton County, 

Kentucky, submitted samples to the Murray State University Breathitt Veterinary Center laboratory (a 

member of the NAHLN) after observing decreased water consumption and increasing mortality in one 

house. The NAHLN laboratory detected H5 and forwarded the samples; NVSL confirmed H5N1 HPAI on 

12 February 2022. Also on 11 February 2022, oropharyngeal swabs from dead chickens and turkeys 

belonging to a mixed-species WOAH poultry [backyard] flock in Fauquier County, Virginia, tested nonnegative for H5 at the Virginia Department of Agriculture and Consumer Services Harrisonburg 

diagnostic laboratory (a member of the NAHLN). The samples were transported to NVSL on 12 February 

2022, where H5 HPAI was confirmed. Subsequently, between 8 February 2022 and 2 March 2022, H5N1 

HPAI was confirmed in seven WOAH poultry [commercial] meat bird turkey premises and one WOAH 

poultry [commercial] broiler production premises in two counties in southern Indiana and two counties 

in western Kentucky (Figure 1). 

ATLANTIC FLYWAY February – March 2022 

Moving to the Atlantic Flyway, on 18 February 2022, the NVSL confirmed clade 2.3.4.4b H5N1 HPAI in a 

non-poultry premises in Suffolk County, New York. This detection was the first of a series of detections 

among WOAH poultry [backyard] premises in Atlantic Flyway States along the Northeastern Atlantic 

coastline (Figure 1); impacted States included Maine, Connecticut, and Massachusetts (Table 1). On 20 

February 2022, one WOAH poultry [commercial] layer hen facility in New Castle County, Delaware, 

observed increased mortality in a single house. Samples from the affected house were collected and 

submitted to the Allen Laboratory at the University of Delaware (a member of the NAHLN) on 21 

February 2022, and H5 was detected the same day. NVSL confirmed HPAI on 22 February 2022. On 3 

March 2022, a table egg layer premises located in Cecil County, Maryland, and within the established 

New Castle Control Area, observed increased mortality. Diagnostic samples were submitted, and the 

NAHLN laboratory detected H5 the same day. The NVSL confirmed H5N1 HPAI the following day. 

Subsequently, six more premises on the Delmarva Peninsula were confirmed between 8 March 2022 

and 18 March 2022. Affected premises types included table egg layer, table egg processing, table egg 

pullet, and broiler production facilities. 

MISSISSIPPI FLYWAY February – May 2022 

Back in the Mississippi Flyway, on 23 February 2022, the NVSL confirmed clade 2.3.4.4b H5N1 HPAI in a 

mixed species WOAH non-poultry flock in Kalamazoo County, Michigan. Subsequently, from 24 March 

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2022 to 10 May 2022, 12 additional premises in Michigan were confirmed; these included 9 WOAH nonpoultry, 2 WOAH poultry [backyard] chicken flocks, and 1 WOAH poultry [commercial] turkey meat bird 

premises. From 1 March 2022 to 18 May 2022, HPAI was confirmed in additional Midwest States located 

in the Mississippi Flyway, including Iowa, Missouri, Illinois, Wisconsin, Minnesota, and Ohio (Table 1; 

Figure 1). HPAI detections in Iowa and Missouri occurred predominately among WOAH poultry 

[commercial] premises. In Iowa, affected premises included nine WOAH poultry [commercial] turkey, six 

WOAH poultry [commercial] table egg layer, and four WOAH non-poultry premises. In Missouri, 

detections included four WOAH poultry [commercial] turkey, one WOAH poultry [commercial] broiler, 

and three non-poultry premises. In Wisconsin, confirmed premises included 7 WOAH poultry 

[commercial] turkey, 1 WOAH poultry [commercial] table egg layer, 1 WOAH poultry [backyard], and 13 

WOAH non-poultry premises. As of 31 May 2022, a total of 80 detections occurred in Minnesota, 

accounting for 22.4 percent of the total cases. Confirmed premises included 57 WOAH poultry 

[commercial] turkey, 1 WOAH poultry [commercial] table egg layer, 1 WOAH poultry [commercial] 

broiler, and 21 WOAH non-poultry producers. Backyard premises in Minnesota included 19 WOAH nonpoultry and 2 WOAH poultry [backyard] premises. HPAI detections in Illinois and Ohio were limited to 

WOAH non-poultry premises. From 8 April 2022 to 19 May 2022, additional confirmations in Indiana 

were reported for three WOAH poultry [commercial] duck premises and two WOAH non-poultry 

premises. 

CENTRAL FLYWAY March 2022 

The first of several poultry premises were affected in the Central Flyway, and on 5 March 2022, the NVSL 

confirmed HPAI on one WOAH poultry [commercial] turkey meat bird premises in Charles Mix County, 

South Dakota. From 12 March 2022 to 20 May 2022, additional detections in South Dakota were 

confirmed for 33 WOAH poultry [commercial] turkey, 1 WOAH poultry [commercial] table egg layer, 1 

WOAH poultry [commercial] gamebird, 2 WOAH poultry [backyard] chicken, and 2 WOAH non-poultry 

premises. Detections in South Dakota accounted for 11.2 percent of all detections in domestic poultry as 

of 31 May 2022, and predominately occurred on the eastern side of the State. Following initial 

detections in South Dakota, subsequent detections were confirmed in Kansas starting 11 March 2022, in 

Nebraska starting 15 March 2022, and in North Dakota starting 29 March 2022. Confirmed detections in 

Kansas included two WOAH non-poultry, three WOAH poultry [backyard], and one WOAH poultry 

[commercial] turkey premises. In Nebraska, the detections included four WOAH non-poultry, two WOAH 

poultry [commercial] broiler, and two WOAH poultry [commercial] table egg layer premises. In North 

Dakota, HPAI affected predominately WOAH poultry [backyard] and WOAH non-poultry premises but 

was also found in four WOAH poultry [commercial] turkey premises. 

ATLANTIC FLYWAY March – May 2022 

While HPAI detections were increasing within the Mississippi and Central Flyways, reports were received 

from previously unaffected States along the east coast in the Atlantic Flyway. These States included 

North Carolina, Pennsylvania, Vermont, and New Jersey. On 29 March 2022, the NVSL confirmed H5 

HPAI in one WOAH poultry [commercial] turkey premises in Johnston County, North Carolina. Active 

surveillance testing for the infection zone identified two additional WOAH poultry [commercial] turkey 

premises. Between 1 April 2022 and 11 April 2022, HPAI was confirmed in three WOAH poultry 

[commercial] turkey and three WOAH poultry [commercial] broiler bird premises in Wayne County, 

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North Carolina. A few days later in Pennsylvania, on 15 April 2022, HPAI was confirmed in one WOAH 

poultry [commercial] table egg layer premises in Lancaster County. The NVSL later confirmed HPAI in 

four additional table egg layer and two WOAH poultry [commercial] broiler premises in Lancaster 

County. On 29 April 2022, the NVSL confirmed HPAI infection in one WOAH poultry [commercial] duck 

facility, which was the first of eight detections of WOAH poultry [commercial] duck premises in 

Lancaster and Berks Counties. Infections were also confirmed for two WOAH poultry [commercial] table 

egg layer premises in Berks County. The confirmed detections in Vermont on 28 April 2022 and in New 

Jersey on 17 May 2022 occurred in WOAH non-poultry premises. 

CENTRAL/PACIFIC FLYWAYS March – May 2022 

Continuing in the Central Flyway and moving into the Pacific Flyway, on 28 March 2022, the NVSL 

confirmed the detection of H5N1 HPAI in one WOAH non-poultry premises in Johnson County, 

Wyoming. This detection represented movement of the outbreak into the Mountain West, which is split 

by the Central and Pacific Flyways (Figure 1). States with confirmed detections included Texas, Montana, 

Colorado, Idaho, Utah, and Oklahoma (Table 1). All confirmations in Wyoming, Montana, and Idaho 

occurred among WOAH poultry [backyard] and WOAH non-poultry premises. In Wyoming, all eight 

detections were WOAH non-poultry premises. In Montana, the detections were among seven WOAH 

non-poultry and two WOAH poultry [backyard] premises. The 25 detections in Idaho included 15 WOAH 

non-poultry, 9 WOAH poultry [backyard], and 1 WOAH poultry [backyard] duck premises. NVSLconfirmed detections in Colorado and Utah included both WOAH non-poultry and WOAH poultry 

premises. In Colorado, two WOAH poultry [backyard], one WOAH poultry [commercial] broiler, one 

WOAH poultry [commercial] table egg layer, and one WOAH non-poultry premises were detected. The 

four detections in Utah included three WOAH non-poultry and one WOAH poultry [commercial] table 

egg layer premises. Detection of HPAI in Texas and Oklahoma was limited to one WOAH poultry 

[commercial] upland game bird and one WOAH poultry [commercial] broiler breeder premises, 

respectively. 

Moving to the west coast, on 29 April 2022, the NVSL confirmed the detection of H5N1 HPAI in one 

WOAH non-poultry premises in Matanuska Susitna, Alaska. This detection represented the first 

detection along the coastline of the Pacific Flyway. On 5 May 2022, HPAI was confirmed in one WOAH 

non-poultry premises in Linn County, Oregon, and one WOAH poultry [backyard] chicken premises in 

Pacific County, Washington. As of 31 May 2022, additional detections occurred in one WOAH poultry 

[backyard] premises in Oregon. 

PACIFIC FLYWAY June 2022 – December 2022 

The number of premises confirmed infected with HPAI decreased during the summer months of June, 

July, and August with an average of 21 (range: 20–22) premises detected per month. Most of these 

detections (48 out of 63) occurred in States within the Pacific Flyway, including Alaska, California, 

Colorado, Montana, Nevada, Oregon, Utah, Washington, and Wyoming (Figure 1). Premises in 

Washington accounted for a third of the summer detections (21 out of 63) and included 11 WOAH nonpoultry and 1 poultry premises in June, 3 WOAH non-poultry and 2 poultry premises in July, and 4 

WOAH non-poultry premises in August. Detections across the U.S. increased during the fall months of 

September, October, and November. However, from September to December, only five additional 

detections occurred in Washington. These detections included one WOAH poultry [commercial] table 

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egg layer, three WOAH non-poultry, and one WOAH poultry [backyard] premises. Confirmed on 14 

December 2022, the table egg layer premises was the first WOAH poultry [commercial] premises 

detected in Washington. Detections in Oregon accounted for almost 15 percent (9 out of 63) of summer 

detections and included one WOAH non-poultry premises detected in June and four WOAH non-poultry 

and four WOAH poultry [backyard] premises detected in July. Subsequently, from 28 September 2022 to 

21 December 2022, the NVSL confirmed detections for 10 WOAH non-poultry and 2 WOAH poultry 

[backyard] premises in Oregon. 

Utah accounted for 10 percent (6 out of 63) of the summer detections. These detections included two 

WOAH non-poultry premises in June, three WOAH poultry [commercial] turkey meat bird premises in 

July, and one WOAH non-poultry premises in August. The 3 WOAH poultry [commercial] turkey meat 

bird premises confirmed infected between 14 July 2022 and 26 July 2022 were the first in a series of 18 

detections in San Pete County, Utah, with the additional 15 premises detected between 13 September 

2022 and 25 October 2022. Between 3 October 2022 and 28 November 2022, the NVSL confirmed 

infections in an additional two WOAH non-poultry and one WOAH poultry [backyard] premises in Utah. 

On 7 July 2022, the NVSL confirmed the first detection in Nevada on a small WOAH non-poultry 

premises in Carson City County, followed by a second detection on 17 October 2022 on one WOAH 

poultry [backyard] premises. The second detection in Alaska, and the first detection since April, was 

confirmed by the NVSL for one WOAH non-poultry premises on 2 August 2022. Subsequent detections in 

Alaska, between 5 October 2022 and 25 November 2022, occurred on an additional four premises, 

including two WOAH poultry [backyard] and two WOAH non-poultry premises. 

Montana, Wyoming, Colorado, and New Mexico are split by the Pacific and Central Flyways. In Montana, 

the NVSL confirmed the detection of one WOAH non-poultry premises within the Pacific Flyway on 26 

July 2022. From 15 September 2022 to 16 December 2022, additional detections in this portion of 

Montana included two WOAH poultry [backyard] and three WOAH non-poultry premises. In the Pacific 

Flyway portion of Colorado, the NVSL confirmed three detections of WOAH non-poultry premises 

between 29 September 2022 to 26 November 2022. No additional detections occurred during the 

summer or fall along the Pacific Flyway in Wyoming or New Mexico. 

On 10 August 2022, the NVSL confirmed the first detection in California on one WOAH non-poultry 

premises located in Sacramento County. This was the first of nine premises in California confirmed 

infected in August, which included two more WOAH non-poultry premises, two WOAH poultry 

[commercial] broiler breeder, and four turkey meat bird premises. From 1 September 2022 to 22 

December 2022, California had an additional 17 premises confirmed infected. These premises included 

three additional WOAH poultry [commercial] broiler breeder, three turkey meat bird, two duck breeder, 

one upland gamebird producer, two WOAH poultry [backyard], and six WOAH non-poultry premises. 

The remaining States in the Pacific Flyway had a combined total of six detections between 12 September 

2022 and 20 December 2022. These included three WOAH non-poultry premises in Idaho confirmed 

infected on 12 September 2022, 20 October 2022, and 20 December 2022, and one WOAH poultry 

[commercial] upland gamebird producer in Idaho confirmed on 21 September 2022. Arizona had two 

WOAH non-poultry premises confirmed infected on 2 November 2022 and 3 November 2022, 

respectively. 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

CENTRAL FLYWAY June 2022 – December 2022 

During the summer months, detections in the Central Flyway included one WOAH non-poultry premises 

in North Dakota confirmed on 6 June 2022 and two WOAH poultry [commercial] table egg premises in 

Weld County, Colorado confirmed on 7 June 2022 and 9 June 2022, respectively. In the fall, additional 

confirmed detections in North Dakota occurred between 1 September 2022 and 10 November 2022, 

including one WOAH poultry [commercial] turkey meat bird, four WOAH poultry [backyard], and four 

WOAH non-poultry premises. In the Central Flyway portion of Colorado, subsequent detections occurred 

from 21 September 2022 to 20 December 2022. These detections included three WOAH poultry 

[commercial] table egg layer, one WOAH poultry [commercial] upland gamebird, two WOAH poultry 

[backyard], and three WOAH non-poultry premises. 

Additional WOAH poultry [commercial] premises detections in the Central Flyway during the fall months 

occurred in Nebraska and South Dakota. From 19 September 2022 to 14 December 2022, Nebraska had 

a total of seven premises confirmed infected. These premises included two WOAH poultry [commercial] 

upland gamebird, one WOAH poultry [commercial] table egg layer, one WOAH poultry [backyard], and 

three WOAH non-poultry premises. Meanwhile, South Dakota had a total of 35 premises confirmed 

infected between 20 September 2022 and 20 December 2022. The detected premises included 20 

WOAH poultry [commercial] turkey meat bird, 3 upland gamebirds, 1 table egg layer, 1 goose breeder, 1 

WOAH poultry [backyard], and 9 WOAH non-poultry premises. 

The NVSL confirmed infections on an additional 11 WOAH non-poultry and 3 WOAH poultry [backyard] 

premises in the Central Flyway, located in Kansas, New Mexico, Oklahoma, Texas, and Wyoming. 

Detections in Texas occurred on three WOAH non-poultry premises between 24 September 2022 and 6 

December 2022. On 4 October 2022, the first and only confirmed detection in New Mexico was on one 

WOAH non-poultry premises in Bernalillo County. In Kansas, detections included three WOAH poultry 

[backyard] premises confirmed between 7 October 2022 and 19 October 2022 and one WOAH nonpoultry premises on 28 December 2022. The detections in the Central Flyway portion of Wyoming 

included two WOAH non-poultry premises and occurred on 12 October 2022 and 7 November 2022, 

respectively. In Oklahoma, the NVSL confirmed three premises between 14 October 2022 and 21 

October 2022 and a fourth premises on 6 December 2022. 

MISSISSIPPI FLYWAY June 2022 – December 2022 

Along the Mississippi Flyway, detections in June were limited to one WOAH poultry [backyard] and one 

WOAH non-poultry premises in Allen County, Indiana. In July, no detections in domestic poultry 

occurred in the Mississippi Flyway. The only detections in August occurred on two WOAH poultry 

[commercial] turkey meat bird premises in Meeker County, Minnesota. Between 1 September 2022 and 

14 December 2022, the NVSL confirmed infection on an additional 28 premises in Minnesota. These 

premises included 18 WOAH poultry [commercial] turkey meat bird, 2 WOAH poultry [commercial] 

turkey breeder hen, and 8 WOAH non-poultry premises. The NVSL confirmed subsequent infections in 

Indiana on 1 September 2022 in one WOAH poultry [backyard] premises and on 13 December 2022 in 

one WOAH poultry [commercial] turkey meat bird premises. Epidemiological investigation identified a 

second WOAH poultry [commercial] turkey meat bird premises in Indiana as a dangerous contact, and 

therefore, this premises was also depopulated. 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

In addition to Indiana and Minnesota, from September 2022 to December 2022, the NVSL confirmed 

detections in 11 of the 12 remaining States in the Mississippi Flyway. Between 2 September 2022 and 7 

November 2022, the NVSL confirmed seven detections in Wisconsin. These detections included three 

WOAH non-poultry, one WOAH poultry [backyard], one WOAH poultry [commercial] duck meat bird, 

one WOAH poultry [commercial] turkey meat bird, and one WOAH poultry [commercial] upland 

gamebird premises. On 3 September 2022, the NVSL confirmed the first WOAH poultry [commercial] 

detection in Ohio on a table egg layer premises in Defiance County. This detection was the beginning of 

a series of first detections along the Mississippi Flyway during the fall months, including the first 

domestic detection in Tennessee on 15 September 2022 in one WOAH poultry [backyard] premises in 

Obion County, the first domestic detection in Arkansas in one WOAH poultry [commercial] broiler 

breeder pullet premises on 7 October 2022 in Madison County, the first domestic detection in 

Mississippi on 4 November 2022 in one WOAH poultry [commercial] broiler breeder in Lawrence 

County, and the first detection in Alabama on 5 December 2022 in one WOAH non-poultry premises in 

Lawrence County. 

Following the first WOAH poultry [commercial] detection in Ohio, the NVSL confirmed infections in four 

WOAH non-poultry premises between 3 September 2022 and 15 September 2022. Additional detections 

in Ohio occurred on 3 October 2022 in one WOAH non-poultry premises and on 7 November 2022 in 

one WOAH poultry [backyard] premises. In Tennessee, seven additional confirmed detections occurred 

between 31 October 2022 and 28 December 2022. These premises included two WOAH poultry 

[backyard], two WOAH non-poultry, and three WOAH poultry [commercial] broiler breeder premises. 

Subsequent detections in Arkansas included two WOAH non-poultry premises confirmed on 14 October 

2022 and 1 December 2022, respectively. Mississippi had one additional WOAH non-poultry premises 

detected on 4 November 2022. 

Fall detections in Michigan, Kentucky, and Illinois occurred on WOAH poultry [backyard] and WOAH 

non-poultry premises. From 13 September 2022 to 12 October 2022, Michigan had four WOAH poultry 

[backyard] and two WOAH non-poultry premises confirmed infected, followed by one WOAH poultry 

[backyard] detection on 10 November 2022 and one WOAH non-poultry detection on 30 December 

2022. One additional WOAH poultry [backyard] premises was a dangerous contact and was 

depopulated. The NVSL confirmed the first detections in Kentucky since the initial detections at the 

beginning of the outbreak on 6 October 2022 in one WOAH poultry [backyard] premises and 11 October 

2022 in one WOAH non-poultry premises. The two confirmed detections in Illinois during the fall 

occurred on 30 November 2022 in one WOAH poultry [backyard] premises and 21 December 2022 in 

one WOAH non-poultry premises. 

The detections in Missouri and Iowa included a mix of WOAH poultry [commercial], WOAH poultry 

[backyard], and WOAH non-poultry premises. On 18 October 2022, the NVSL confirmed the first fall 

detection in Missouri on one WOAH non-poultry premises. Seven subsequent detections occurred 

between 22 November 2022 and 21 December 2022 and included four WOAH non-poultry, two WOAH 

poultry [commercial] turkey meat bird, and one WOAH poultry [backyard] premises. The NVSL 

confirmed infected a total of 11 premises in Iowa between 20 October 2022 and 12 December 2022. 

From 20 October 2022 to 8 November 2022, confirmed detections included two WOAH non-poultry and 

51 USDA APHIS 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

two WOAH poultry [commercial] table egg premises. From 5 December 2022 to 12 December 2022, the 

detections included seven WOAH poultry [commercial] turkey meat bird premises. 

ATLANTIC FLYWAY June 2022 – December 2022 

During the summer months of June, July, and August, the NVSL confirmed infected a total of eight 

premises along the Atlantic Flyway (Figure 1). These detections included two WOAH non-poultry 

premises in Georgia, one WOAH poultry [commercial] duck and one WOAH poultry [backyard] premise 

in Pennsylvania, one WOAH non-poultry premises in Maine, two WOAH non-poultry premises in Florida, 

and one WOAH non-poultry premises in Virginia. The confirmed infection of one WOAH non-poultry 

premises on 1 June 2022 in Toombs County was the first detection in Georgia during this outbreak; the 

second confirmed infection occurred on 22 August 2022 in Henry County. In Pennsylvania, one WOAH 

poultry [commercial] duck premises confirmed infected on 2 June 2022 was the last premises in a 

cluster of WOAH poultry [commercial] duck premises in Berks County. The WOAH non-poultry premises 

in Virginia confirmed infected on 27 August 2022 was the first detection in Virginia since the detection at 

the beginning of the outbreak. 

From September 2022 to December 2022, the NVSL confirmed an additional 65 premises infected along 

the Atlantic Flyway (Figure 1). Between 18 September 2022 and 17 November 2022, Pennsylvania had 

an additional 17 premises confirmed infected. These detections included eight WOAH poultry 

[commercial] turkey, four WOAH poultry [backyard], and seven WOAH non-poultry premises. Two 

additional WOAH poultry [backyard] premises were dangerous contacts and depopulated. Among the 

eight WOAH poultry [commercial] turkey premises was a cluster of six premises confirmed between 1 

November 2022 and 9 November 2022. In Maine, the confirmed detection of one additional WOAH nonpoultry premises occurred on 21 November 2022. Subsequent detections in Florida accounted for 32 

percent (21 out of 65) of infections along the Atlantic Flyway. From 11 October 2022 to 16 December 

2022, the NVSL confirmed detections on 3 WOAH poultry [backyard] and 18 WOAH non-poultry 

premises. In Virginia, four additional confirmed infections of WOAH non-poultry premises happened 

between 5 October 2022 and 4 November 2022. 

Aside from the detections in Maine, the NVSL confirmed an additional 16 fall detections in the 

northeastern portion of the Atlantic Flyway. These detections included 1 WOAH poultry [commercial], 

13 WOAH non-poultry, and 2 WOAH poultry [backyard] premises. In Massachusetts, detections of two 

WOAH non-poultry premises were confirmed on 15 September 2022 and 3 November 2022, 

respectively. Maryland’s detections included one WOAH non-poultry premises on 22 September 2022 

and one WOAH poultry [commercial] table egg breeder on 29 November 2022. New Hampshire had one 

WOAH poultry [backyard] premises confirmed infected on 23 September 2022. Delaware had two 

WOAH non-poultry premises confirmed on 24 September 2022. Confirmed infections of WOAH nonpoultry premises occurred in Connecticut on 5 October 2022, in Rhode Island on 20 October 2022, and 

in Vermont on 6 December 2022. The NVSL also confirmed the infections of three WOAH non-poultry 

premises in New Jersey between 13 October 2022 and 2 November 2022. Detections in New York 

included two WOAH non-poultry premises confirmed on 1 November 2022 and 4 November 2022 and 

one WOAH poultry [backyard] premises confirmed on 12 November 2022. 

An additional six detections occurred in the southern portion of the Atlantic Flyway in North Carolina 

and South Carolina. Between 21 October 2022 and 9 December 2022, the NVSL confirmed the infection 

52 USDA APHIS 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

of five WOAH non-poultry premises in North Carolina. On 3 November 2022, the NVSL confirmed the 

first and only domestic detection in South Carolina in one WOAH non-poultry premises in Beaufort 

County. 

PACIFIC FLYWAY January 2023 – March 2023 

Following the increase in confirmed HPAI detections during the fall months, the number of infections 

dropped at the beginning of 2023. The NVSL confirmed 99 cases between January and the end of March, 

including 28 infections in January, 31 infections in February, and 40 infections in March (Figure 2). The 

Pacific Flyway had a total of 21 confirmed infections, including 19 WOAH non-poultry, 1 WOAH poultry 

[backyard], and 1 WOAH poultry [commercial] duck breeder premises (Figure 1). The 19 WOAH nonpoultry premises included 7 in California, 5 in Oregon, 3 in Washington, and 1 premises each in 

Montana, Colorado, Nevada, and Idaho. The one WOAH poultry [backyard] and one WOAH poultry 

[commercial] duck premises detections occurred in California on 12 January 2023 and 6 February 2023, 

respectively. 

CENTRAL FLYWAY January 2023 – March 2023 

In the Central Flyway, the NVSL confirmed 16 detections between January and March 2023 (Figure 1). 

These detections included eight WOAH non-poultry, four WOAH poultry [backyard], and four WOAH 

poultry [commercial] upland gamebird premises located in Kansas, South Dakota, Colorado, Nebraska, 

and Texas. The detections in Kansas included three WOAH poultry [commercial] upland gamebird 

premises confirmed between 4 January 2023 and 8 February 2023, and two WOAH non-poultry 

premises confirmed on 13 February 2023 and 24 March 2023, respectively. South Dakota had one 

WOAH poultry [backyard] premises confirmed on 5 January 2023 and one WOAH poultry [commercial] 

upland gamebird premises confirmed infected on 22 March 2023. In the Central Flyway portion of 

Colorado, the NVSL confirmed two WOAH non-poultry premises in January 2023 and one WOAH nonpoultry and one WOAH poultry [backyard] premises in March 2023. In Nebraska, two confirmed 

detections included one WOAH non-poultry premises on 9 January 2023 and one WOAH poultry 

[backyard] premises on 21 February 2023. Texas also had two confirmed detections, one WOAH poultry 

[backyard] premises on 18 January 2023 and one WOAH non-poultry premises on 22 March 2023. The 

detection confirmed in the Central Flyway portion of Wyoming occurred on 6 February 2023 on one 

WOAH non-poultry premises. 

MISSISSIPPI FLYWAY January 2023 – March 2023 

From January 2023 to March 2023, the NVSL confirmed 13 cases of HPAI along the Mississippi Flyway 

(Figure 1). These premises included two WOAH poultry [commercial] broiler, two WOAH poultry 

[commercial] turkey meat bird, seven WOAH non-poultry, and two WOAH poultry [backyard] premises. 

Detections in Missouri and Ohio were limited to WOAH non-poultry premises. Missouri had three WOAH 

non-poultry premises confirmed on 4 January 2023, 13 February 2023, and 16 March 2023. Ohio had 

one premises confirmed on 18 January 2023. In Tennessee, the NVSL confirmed one WOAH poultry 

[commercial] broiler production premises on 20 January 2023. While this premises was geographically 

close to the broiler breeder premises detected at the end of December 2022 in Kentucky, phylogenetic 

sequencing and lack of epidemiological evidence suggested it was an independent wild-bird 

introduction. The two NVSL-confirmed WOAH poultry [commercial] turkey premises were independent 

53 USDA APHIS 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

cases and occurred in Iowa on 25 January 2023 and in Illinois on 24 February 2023. In Iowa, the NVSL 

also confirmed the infection of one WOAH non-poultry premises on 15 March 2023. Premises confirmed 

in Mississippi included one WOAH poultry [commercial] broiler production on 7 February 2023, one 

WOAH poultry [backyard] premises on 17 February 2023, and one WOAH non-poultry premises on 16 

March 2023. One additional WOAH poultry [commercial] broiler premises in Mississippi was 

depopulated as a dangerous contact. Confirmed detections in Michigan included one WOAH non-poultry 

premises on 14 March 2023 and one WOAH poultry [backyard] premises on 23 March 2023. 

ATLANTIC FLYWAY January 2023 – March 2023 

NVSL-confirmed detections along the Atlantic Flyway accounted for 49 percent (49 out of 99) of the 

infections between January 2023 and March 2023 (Figure 1). Detections occurred in Virginia, New 

Hampshire, North Carolina, New York, Maine, Pennsylvania, and Florida and included 25 WOAH poultry 

[backyard], 12 WOAH non-poultry, 4 WOAH poultry [live bird market], 5 WOAH poultry [commercial] 

turkey, 2 WOAH poultry [commercial] duck, and 1 WOAH poultry [commercial] broiler premises. In 

Virginia, infected premises included two WOAH poultry [commercial] turkey meat bird premises 

confirmed on 19 January 2023 and 25 January 2023, respectively, and one WOAH non-poultry premises 

confirmed on 6 March 2023 in Rockingham County. Confirmed infections of one WOAH non-poultry 

premises occurred in New Hampshire on 20 January 2023 and in North Carolina on 23 January 2023. In 

Maine, the NVSL confirmed the infections of three additional WOAH non-poultry premises between 26 

January 2023 and 1 February 2023. Confirmed detections in New York included one WOAH non-poultry 

premises on 25 January 2023, one WOAH poultry [backyard] premises on 15 February 2023, and one 

WOAH poultry [backyard] game farm on 22 March 2023. 

The majority of the detections (32 out of 49) occurred in Pennsylvania, and included 23 WOAH poultry 

[backyard], 3 WOAH non-poultry, 3 WOAH poultry [commercial] turkey, 2 WOAH poultry [commercial] 

duck, and 1 WOAH poultry [commercial] broiler premises. Lancaster County had 23 of these detections, 

Chester County had 4, and the remaining 5 were individual county detections. The localized outbreak 

was largely attributed to lateral spread associated with the sale of infected birds through the live bird 

market (LBM) and the delayed reporting of sick birds. To get the outbreak under control, the 

Pennsylvania Department of Agriculture temporarily shut down live bird markets and later issued a 

general quarantine order mandating weekly testing for LBM-associated premises in specific townships. 

This response led to an immediate decline in the number of new detections within the LBM system and 

effectively prevented further lateral spread between markets. Spread through the LBM was also 

responsible for the infection of an LBM premises in Virginia confirmed on 23 February 2023 and an LBM 

premises in New York confirmed on 22 March 2023. The remaining three confirmed premises were 

located in Florida and included one WOAH non-poultry premises confirmed on 14 February 2023 and 

two LBM premises confirmed on 28 February 2023 and 21 March 2023. Phylogenetics determined the 

viral genotype responsible for the infection of these LBM premises was a different genotype than the 

other LBM premises. 

54 USDA APHIS 
 

 

Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Figure A1. Weekly confirmed detections of highly pathogenic avian influenza by reportable species and wild 

migratory bird flyways as of 31 March 2023. 

55 USDA APHIS 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Table A1. Confirmed detections of highly pathogenic avian influenza by State as of 31 March 2023. 

Total First Last State Detections Detection Detection 

Chicken Turkey Duck Pheasant Goose Other* 

Alabama 1 12/5/2022 12/5/2022 

Alaska 6 4/29/2022 11/25/2022 5 

Arizona 2 11/2/2022 11/3/2022 2 

Arkansas 3 10/7/2022 12/1/2022 2 

California 35 8/10/2022 2/17/2023 20 7 5 2 1 

Colorado 24 4/8/2022 3/28/2023 16 1 1 1 5 

Connecticut 2 3/1/2022 10/5/2022 1 1 

Delaware 5 2/22/2022 9/24/2022 3 

Florida 26 7/21/2022 3/21/2023 23 1 2 

Georgia 2 6/1/2022 8/22/2022 

Idaho 30 4/14/2022 3/6/2023 20 1 1 1 7 

Illinois 7 3/11/2022 2/24/2023 3 1 1 1 1 

Indiana 15 2/8/2022 12/13/2022 2 7 3 3 

Iowa 32 3/1/2022 3/15/2023 13 17 

Kansas 15 3/11/2022 3/24/2023 7 1 1 3 1 2 

Kentucky 4 2/12/2022 10/11/2022 1 1 

Maine 17 2/19/2022 2/6/2023 15 1 1 

Maryland 6 3/4/2022 11/29/2022 5 

Massachusetts 3 3/29/2022 11/3/2022 1 1 1 

Michigan 23 2/23/2022 3/23/2023 16 2 3 2 

Minnesota 110 3/25/2022 12/14/2022 28 79 1 2 

Mississippi 5 11/4/2022 3/16/2023 3 1 1 

Missouri 20 3/4/2022 3/16/2023 8 7 5 

Montana 16 4/7/2022 1/10/2023 4 1 

Nebraska 17 3/15/2022 2/21/2023 14 2 1 

Nevada 3 7/7/2022 3/3/2023 3 

New Hampshire 3 3/16/2022 1/23/2023 3 

New Jersey 4 5/17/2022 11/2/2022 

New Mexico 1 10/4/2022 10/4/2022 1 

New York 16 2/18/2022 3/22/2023 8 

North Carolina 15 3/29/2022 1/25/2023 7 6 1 1 

North Dakota 24 3/29/2022 11/10/2022 12 5 

Ohio 9 3/29/2022 1/18/2023 6 1 2 

Oklahoma 5 4/30/2022 12/6/2022 2 

Oregon 28 5/5/2022 3/30/2023 15 4 1 8 

Pennsylvania 67 4/15/2022 3/17/2023 19 12 21 1 14 

Rhode Island 1 10/20/2022 10/20/2022 1 

South Carolina 1 11/3/2022 11/3/2022 1 

1 

1 

1 

2 

1 1 

2 

2 

1 

11 

1 3 

2 6 

7 

1 2 

56 USDA APHIS 
Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Total First Last State Detections Detection Detection 

Chicken Turkey Duck Pheasant Goose Other* 

South Dakota 77 3/5/2022 3/22/2023 13 

Tennessee 9 9/15/2022 1/20/2023 9 

Texas 6 4/2/2022 3/22/2023 4 1 1 

Utah 28 4/15/2022 11/28/2022 7 18 1 2 

Vermont 2 4/28/2022 12/6/2022 1 1 

Virginia 10 2/12/2022 3/7/2023 2 2 1 1 4 

Washington 42 5/5/2022 2/14/2023 25 8 2 7 

Wisconsin 29 3/14/2022 11/7/2022 4 8 1 1 15 

Wyoming 11 3/29/2022 2/6/2023 11 

53 5 1 5 

Total 817 365 228 63 24 13 22 

 

 

 

 

*Other species includes assorted pet birds, chukars, ratites, multiple poultry species, and “other poultry” designations. 

57 USDA APHIS 
 

 

 

 

 

 

 

 

 

 

 

 

 

Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

APPENDIX B: INITIAL CONTACT EPIDEMIOLOGICAL REPORT 

HPAI Response 

Initial Contact Epidemiological (Epi) Report 

June 27, 2016 

I. PREMISES INFORMATION 

Premises Identification Number: 

Name of Premises: 

Owner of Premises: 

Address of Premises: 

County of Premises: 

Premises Owner Phone: 

Premises Owner Email: 

Premises Entrance Latitude: 

Premises Entrance Longitude: 

II. OWNER INFORMATION 

Owner of Animals: 

Address of Animal Owner: 

Animal Owner Phone: 

Animal Owner Email: 

III. INTERVIEW CONTACT INFORMATION 

Name of person administering questionnaire: 

Name of person answering questionnaire: 

Phone: 

Position (e.g., owner, manager, veterinarian, etc.): 

Date of interview: 

IV. FLOCK INFORMATION 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Clinical signs (brief description) 

Baseline daily mortality rate: (insert rate from farm 

records) 

Daily mortality rate (# of dead birds/bird population on 

date of initial sampling) 

Date first clinical signs were noted 

Date initial samples were collected 

Laboratory to which initial samples were submitted 

Results of any AI tests in past 21 days 

Date premises quarantine or hold order was issued 

House ID Type of Birds Number of 

Birds 

Age of 

Birds 

House 

Dimensions 

Ceiling Height Ventilation 

Type 

Date of Onset of 

Clinical Signs 

Do you have a veterinarian who regularly advises you on disease prevention?  Yes  No 

If yes, name of veterinarian: 

Do you have a pre-arranged depopulation plan for this flock?  Yes  No 

If yes, briefly describe the pre-arranged depopulation method: 

Have you exercised or used this method previously?  Yes  No 

V. TRACE-IN AND TRACE-OUT QUESTIONNAIRE 

Name of person administering questionnaire: _______________________________________________ 

Name of person answering questionnaire: __________________________________________________ 

Phone: _______________________________________________________________________________ 

Position (e.g., owner, manager, veterinarian, etc.): ____________________________________________ 

1. How are dead birds (daily mortality) disposed of on this farm (please circle one or 

more)? Also specify if disposal occurs on or off this premises. 

a. Composting 

b. Burial 

c. Incineration 

d. Rendering 

e. Landfill 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Other (specify): 

If disposal occurs at another premises: 

Name and Location (company name) Transported by 

2. List any locations that accept manure/litter from this premises during the last 21 days. 

Name and location (company name) Date (mm/dd/yy) Intended use 

3. Was manure or animal material from another premises brought onto this premises 

during the last 21 days? 

 Yes  No 

If Yes, 

Product Source Date (mm/dd/yy) 

4. Have you or any of your employees (including any contractors or volunteers) visited any other 

premises with poultry or any processors of eggs or poultry products during the last 21 days 

(e.g., farm, slaughter, processing, market, residence with poultry)? 

 Yes  No 

If Yes, 

Premises/processor name Person/title Date (mm/dd/yy) 

5. Is there a community living situation where farm workers from this premises interact with 

workers from other poultry facilities? 

 Yes  No 

If Yes, describe: 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

6. Did any crews (e.g., catch crews, load-out, vaccination, insemination) enter the premises 

during the last 21 days? 

 Yes  No 

If Yes, 

Crew type Date (mm/dd/yy) Name/company 

7. Did any of the following visit the premises during the last 21 days? 

If Yes, give date and name or company information. 

Visitor type Date (mm/dd/yy) Name/company 

a. Federal/State veterinary or animal health 

worker 

b. Extension agent or university veterinarian 

c. Private or company veterinarian 

d. Company service person 

e. Nutritionist or feed company consultant 

f. Inspector (e.g., FDA, NOP, biosecurity 

auditor, etc.) 

g. Feed delivery 

h. Egg truck 

i. Litter/bedding delivery 

j. Litter removal 

k. Renderer/dead bird pick up 

l. Pest/rodent control 

m. Manure truck 

n. Trash pick up 

o. Occasional worker (e.g., family member, 

part-time help over holiday) 

p. Wholesaler, buyer, or dealer 

q. Customer/consumer (private individual) 

r. Other 

8. Specify if any equipment was shared with another premises during the last 21 days, 

whether you received or loaned the equipment, and the location and name of the 

companies or premises the equipment was shared with: 

Vehicle Received/loaned Specify (name, company, location) 

61 USDA APHIS 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

ATV/4-wheeler  Rec’d  Loaned 

Tractor  Rec’d  Loaned 

Gates/panels  Rec’d  Loaned 

Skid-steer loaders  Rec’d  Loaned 

Egg flats  Rec’d  Loaned 

Egg racks  Rec’d  Loaned 

Pallets  Rec’d  Loaned 

Dead bird containers  Rec’d  Loaned 

Manure/litter handling equipment  Rec’d  Loaned 

Pressure sprayers/ washers/foamers  Rec’d  Loaned 

Other cleaning equipment  Rec’d  Loaned 

Vaccination equipment  Rec’d  Loaned 

Bird catching equipment  Rec’d  Loaned 

Live haul loader  Rec’d  Loaned 

Other (specify: ___________________)  Rec’d  Loaned 

9. Were any birds introduced onto the premises during the last 21 days? 

 Yes  No 

If Yes, 

Date (mm/dd/yy) Bird type (e.g., chicks, poults, spiking 

roosters, layers, breeders, etc.) 

Source Transported by 

10. Have any birds moved off the premises during the last 21 days? 

 Yes  No 

If Yes, 

Date (mm/dd/yy) Bird type (e.g., chicks, poults, spiking 

roosters, layers, breeders, etc.) 

Destination Transported by 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

11. Were any birds moved within the premises during the last 21 days? (e.g., from one barn to 

another on the same premises) 

 Yes  No 

If Yes, 

a. Was a contract crew used? 

 Yes  No 

If Yes, specify company/crew name: 

b. Was farm specific equipment used? 

 Yes  No 

If No, describe: 

12. Were any eggs moved onto the premises during the last 21 days? 

 Yes  No 

If Yes, 

a. List source (name and location) for eggs coming onto this premises during the last 

21 days, the dates eggs were received, and whether the eggs were intended for 

hatching, or were processed or unprocessed from source. 

Source name and location 

(company name) 

Date (mm/dd/yy) Intended for 

hatching? 

Processed?* 

 Yes  No  Yes  No 

 Yes  No  Yes  No 

 Yes  No  Yes  No 

 Yes  No  Yes  No 

 Yes  No  Yes  No 

*Method of processing: _________________ 

13. Were any eggs moved off the premises during the last 21 days? 

 Yes  No 

If Yes, 

a. List source (name and location) for eggs moving off this premises during the last 21 

days, the dates eggs left, and whether the eggs were intended for hatching, or were 

processed or unprocessed from source. 

Source name and location 

(company name) 

Date (mm/dd/yy) Intended for 

hatching? 

Processed?* 

 Yes  No  Yes  No 

 Yes  No  Yes  No 

 Yes  No  Yes  No 

 Yes  No  Yes  No 

 Yes  No  Yes  No 

*Method of processing: _________________ 

14. Is there any additional or important information that we need to know at this time regarding the 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

disease on your farm? 

 Yes  No 

If Yes, describe: ___________________________________________________________ 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

APPENDIX C: COMMERCIAL TURKEY CASE CONTROL SURVEY 

UNITED STATES DEPARTMENT OF AGRICULTURE 

ANIMAL AND PLANT HEALTH INSPECTION SERVICE 

VETERINARY SERVICES 

2150 CENTRE AVE, BLDG B 

FORT COLLINS, CO 80526 

COMMERCIAL TURKEY CASE 

CONTROL SURVEY 

According to the Paperwork Reduction Act of 1995, an agency may not conduct or sponsor, and a person 

is not required to respond to a collection of information unless it displays a valid OMB control number. 

The valid OMB control number for this information collection is 0579-0484. The time required to complete 

this information collection is estimated to average 75 minutes per response, including the time to review 

instructions, search existing data resources, gather the data needed, and complete and review the 

information collected. 

OMB Approved 

0579-0484 

EXP: 04/30/2023 

The information you provide will be used for statistical purposes only. Your responses will be kept confidential and any person who 

willfully discloses ANY identifiable information about you or your operation is subject to a jail term, a fine, or both. This survey is 

conducted in accordance with the Confidential Information Protection and Statistical Efficiency Act of 2018, Title III of Pub. L. No. 

115-435, codified in 44 U.S.C. Ch. 35 and other applicable Federal laws. For more information on how we protect your information 

please visit: https://www.nass.usda.gov/confidentiality. Response is voluntary. 

Date (mm/dd/yy): _______________date 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Section A – Case or Control 

1. Is this a case or control farm? [During the interview, verify the farm name and address printed on the 

label are correct for this farm.] t101 

1 Case farm [Go to Item 2.] 

3 Control farm [Go to Item 3.] 

2. If this is a case farm, 

a. The following is the 14-day reference period for this farm: 

t102/t102a ________________ – _______________ mm/dd/yy – mm/dd/yy 

In this questionnaire, we will ask many questions about a 14-day reference period. The “reference period” 

for your farm is the 14 days between [Insert the dates listed in Item 2a above]. This is the 14 days before the 

detection of HPAI on this farm. 

b. How many turkeys were on this farm on the last day of the reference period? t103 ______ # turkeys 

c. During the 2022 HPAI outbreak, how many of the barns on this farm were confirmed or were suspected to 

be infected with HPAI? ................................................................................. t104 __________# barns 

[Go to Section B.] 

3. If this is a control farm, 

a. The tentative 14-day reference period for this farm is: 

t105/t105a _______________ – ______________ mm/dd/yy – mm/dd/yy 

b. Did you have turkeys for the entire 14-day period between the dates in Item 3a above? t106 

1 Yes 

3 No 

If Yes, the “14-day reference period” for your farm is [Insert the dates listed in Item 3a above]. We will 

refer to this as the “reference period” throughout the questionnaire. [Proceed to Item 3c.] 

If No, help the producer identify the closest 14-day period to the reference period from Item 3a during 

which they had turkeys on the farm and enter that period into the fields below. This period must be during 

2022. 

Enter the selected 14-day period here: t107 Start date ____________ mm/dd/yy 

(Finish date = start date + 14 days) t108 Finish date ___________ mm/dd/yy 

All questions regarding the “reference period” refer to the 14 days selected above. We will refer to this as 

the “reference period” throughout the questionnaire. 

[If the farm did not have turkeys during 2022, go to Section L.] 

c. How many turkeys were on this farm on the last day of the reference period? t109 ______ # turkeys 

Section B – Premises Description 

1. What stage(s) of turkey production is on this farm? 

a. Brooder ........................................................................................................t201 1 Yes 3 No 

b. Grower ........................................................................................................t202 1 Yes 3 No 

c. Breeder ........................................................................................................t203 1 Yes 3 No 

d. Other (specify: _____________________) t204oth.......................................t204 1 Yes 3 No 

2. What is the sex of the market type on this farm? [Check all that apply.] 

1 Hens t205 

1 Toms t206 

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1 Breeder hens t207 

1 Breeder toms t208 

3. Is this farm multiple age or single age? [Check one only.] t209 

1 Multiple age 

2 Single age 

4. What other type(s) of poultry is present on this farm? 

a. Broiler ........................................................................................................t210 1 Yes 3 No 

b. Layer ........................................................................................................t211 1 Yes 3 No 

c. Domestic ducks or geese (exclude wild birds) ............................................t212 1 Yes 3 No 

d. Other (specify: _____________________) t213oth.......................................t213 1 Yes 3 No 

5. Is this farm certified organic? .............................................................................t214 1 Yes 3 No 

6. Is this facility enrolled in NPIP?..........................................................................t215 1 Yes 3 No 

a. If yes, is this facility enrolled in an NPIP Avian Influenza Program?...........t216 1 Yes 3 No 

7. Is this a: [Check one only.] t217 

1 Company farm? 

2 Contract farm? 

3 Independent farm? 

4 Other? (specify:_______________________________ ) t217oth 

8. How many barns are on this farm? .......................................................................... t218 ___________# barns 

a. In the last year, how many of these barns housed birds? ....................................t219 ___________# barns 

For the remainder of the questionnaire, some questions will ask about practices for the entire farm, and 

other questions will ask about practices for a “selected barn.” 

INSTRUCTIONS for selecting a barn: 

Case farm: Select the first barn on this premises that was confirmed to be HPAI positive. If more than one barn 

was confirmed to be HPAI positive on the same date, choose one barn. Answer questions for the 14 days prior 

to the onset of clinical signs or increased mortality (the reference period). [Section A, Item 2a] 

Control farm: Randomly select one barn to be the “selected barn.” Choose one that had birds during the 14-day 

reference period [Section A, Item 3]. Use this barn to answer all questions about the “selected barn.” 

9. What is the barn ID or name for the selected barn? ........................................t220 _______________________ 

10. During the 14-day reference period, did any birds on the farm or selected barn have access to the outdoors? 

a. Any birds on the farm ..................................................................................t221 1 Yes 3 No 

b. Selected barn .............................................................................................t222 1 Yes 3 No 

11. Were any livestock, excluding poultry, on the farm, or located within 350 yards of the farm, fed hay or grain in 

the pasture or in outdoor feed troughs during the 14-day reference period? 

(350 yards is about the length of three football fields.)...............t223 1 Yes 3 No 4 Don’t Know 

12. What is the water source for poultry? 

a. Off-site fresh water (for example, municipal, federal, cooperative, 

community, commercial)..............................................................................t224 1 Yes 3 No 

b. Well..............................................................................................................t225 1 Yes 3 No 

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c. Surface water (for example, pond) ..............................................................t226 1 Yes 3 No 

d. Other (specify: _____________________) t228oth ......................................t227 1 Yes 3 No 

13. Are water treatments such as chlorination used in the drinking water for the poultry on this farm? 

t228 1 Yes 3 No 

a. If Yes, are these treatments given: ..............................t229 1 Continuously? 3 Intermittently? 

14. Are windbreaks present on this farm? 

Windbreak type Present? 

If Yes, distance to 

closest poultry barn 

a. Evergreen or juniper 1 Yes 3 No _______ yards 

b. Deciduous tree 1 Yes 3 No _______ yards 

c. Structural (for example, hill, natural 

break) 1 Yes 3 No _______ yards 

t230/t233 

t231/t234 

t232/t235 

15. Are the following water body type(s) visible or within 350 yards (about three football fields) of this farm? 

a. Pond ............................................................................................................t236 1 Yes 3 No 

b. Lake .............................................................................................................t237 1 Yes 3 No 

c. Stream .........................................................................................................t238 1 Yes 3 No 

d. River ............................................................................................................t239 1 Yes 3 No 

e. Wetland or swamp.......................................................................................t240 1 Yes 3 No 

f. Wastewater lagoon......................................................................................t241 1 Yes 3 No 

g. Standing water during the 14-day reference period ....................................t242 1 Yes 3 No 

h. Drainage ditch or canal................................................................................t243 1 Yes 3 No 

i. Other (specify: _____________________) t245oth.......................................t244 1 Yes 3 No 

[If Question 15 a through i are all equal to No, skip to Question 17.] 

16. For those water bodies, including drainage ditches and lagoons within 350 yards on the farm, approximately 

how many wild waterfowl or shorebirds (for example, ducks, geese, wading birds, gulls) were seen on the 

water during the 14-day reference period? [Check one only.] t245 

1 None 2 Tens 3 Hundreds 4 Thousands 5 Don’t know 

17. What is the distance (in yards) of the closest body of water (for example, pond, lake, stream, river, wetland) to 

this farm? t246 ...........................................................................................................yards 

18. In the 14-day reference period, approximately how many wild waterfowl or shorebirds (for example, ducks, 

geese, wading birds, gulls) might have been seen on this body of water at one time? [Check one only.] t247 

1 None 2 Tens 3 Hundreds 4 Thousands 5 Don’t know 

19. What is the approximate distance (in yards) to the closest field where crops or hay are harvested? 

t248 _____________yards 

20. What crop was last grown in this field? [Check one only.] t249 

1 Corn 

2 Soybeans 

3 Alfalfa or grass intended for livestock feed 

4 Other (specify:________________________________ ) t250oth 

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5 Don’t know

21. Was this field tilled in:

a. Fall 2021? .................................................................. t250 1 Yes 3 No 4 Don’t know 

b. Spring 2022? .............................................................. t251 1 Yes 3 No 4 Don’t know 

22. Was this field actively worked (for example, tilled, disked, hay harvested, trees cut, row crops harvested)

during the 14-day reference period?...........................................t252 1 Yes 3 No 4 Don’t know 

23. For this closest field, approximately how many wild waterfowl or shorebirds (for example, ducks, geese,

wading birds, gulls) were seen during the 14-day reference period? [Check one only.] t253 

1 None 2 Tens 3 Hundreds 4 Thousands 5 Don’t know

Section C – Wild Birds 

1. During the 14-day reference period, how frequently were the following types of wild birds seen on the farm

and within 100 yards of the outside of the barns?

Bird type Often Sometimes Never 

a. Waterfowl (for example, ducks, geese) 1 2 3 

b. Gulls 1 2 3 

c. Small perching birds (for example, sparrows,

starlings, swallows) 1 2 3 

d. Blackbirds and crows 1 2 3 

e. Other water birds (for example, egrets,

cormorants) 1 2 3 

f. Wild turkeys, pheasants, quail 1 2 3 

g. Raptors (for example, eagles, hawks, owls,

vultures) 1 2 3 

h. Pigeons and doves 1 2 3 

i. Other (specify:_________________) t309oth 1 2 3 

t301 

t302 

t303 

t304 

t305 

t306 

t307 

t308 

t309 

2. During the 14-day reference period, how frequently were the following types of wild birds seen inside the

selected barn?

Bird type Often Sometimes Never 

a. Large birds (for example, pigeons, crows) 1 2 3 

b. Small birds (for example, finches, sparrows,

starlings) 1 2 3 

c. Other (specify: ________________ ) t312oth 1 2 3 

t310 

t311 

t312 

3. During the 14-day reference period, did you or other farm workers observe any of the following types of sick

or dead wild birds inside the barns or outside of the barns?

Inside the Outside the 

Sick/dead bird type barns barns 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

a. Large birds (for example, pigeons, crows) 1 Yes 3 No 1 Yes 3 No 

b. Small birds (for example, finches, sparrows, 

starlings) 1 Yes 3 No 1 Yes 3 No 

c. Other (specify: ________________ ) t315oth 1 Yes 3 No 1 Yes 3 No 

t313/t316 

t314/t317 

t315/t318 

4. If Yes to Questions 3a, 3b, or 3c, what was done with the sick or dead wild birds? 

a. Left for predators .........................................................................................t319 1 Yes 3 No 

b. Disposal by same method used for daily turkey mortality on farm..............t320 1 Yes 3 No 

c. Taken to rehab center, animal control or veterinarian.................................t321 1 Yes 3 No 

d. Something else (specify: ___________________ ) t322oth..........................t322 1 Yes 3 No 

Section D – Farm Biosecurity 

1. What best describes the road surface on this farm that vehicles coming onto the operation drive on? [Check 

one only.] t401 

1 Hard top/asphalt 

2 Gravel 

3 Dirt 

4 Other (specify: _______________________________ ) t401oth 

2. In general, do the following types of vehicles: 

Codes for question 2 

1 = come to the perimeter of the farm only 

2 = enter the farm but not near the barns 

3 = come near the barns 

4 = do not come at all 

Enter the codes that apply. 

a. Garbage or dumpster pick up......................................................................t402 ______code 

b. Propane delivery..........................................................................................t403 ______code 

c. Feed delivery ...............................................................................................t404 ______code 

d. Feed ingredient delivery ..............................................................................t405 ______code 

e. Renderer......................................................................................................t406 ______code 

f. Company personnel (for example, catch/vaccination crew, barn workers, 

service person, veterinarian) .......................................................................t407 ______code 

g. Other business visitors (for example, meter reader, repairman).................t408 ______code 

3. In general, how many vehicles (including employee vehicles) come to the following locations on a weekly 

basis? 

a. Perimeter of the farm only ............................................................. t409 _________ vehicles per week 

b. Enter the farm but not near the barns............................................ t410 _________ vehicles per week 

c. Come near the barns..................................................................... t411 _________ vehicles per week 

4. Excluding driveways on farm, what is the distance (in yards or miles) from this farm to the nearest public 

gravel or dirt road? .................................................................t412y ____________ yards OR t412m ______________ miles 

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5. How frequently is vegetation mowed and/or bush hogged on the premises? 

(Answer for when vegetation is present, for example, spring and summer)......t413 ______ times/month 

6. Was there a wash station or spray area being used for vehicles during the 14-day reference period? 

t414 1 Yes 3 No 

[If Question 6 = No, SKIP to Question 8.] 

7. During the 14-day reference period, was the vehicle wash station or spray area: 

a. Located on the farm?...................................................................................t415 1 Yes 3 No 

b. Were the vehicle tires washed?...................................................................t416 1 Yes 3 No 

c. Was the vehicle exterior washed?...............................................................t417 1 Yes 3 No 

d. Was the vehicle interior cleaned (for example, floor mats) .........................t418 1 Yes 3 No 

e. Were the following vehicles washed? 

i. Worker vehicles............................................................................ t419 1 Yes 3 No 4 NA 

ii. Feed trucks .................................................................................. t420 1 Yes 3 No 4 NA 

iii. Vehicles delivering or removing birds .......................................... t421 1 Yes 3 No 4 NA 

iv. Other vehicles (specify: _________________ ) t422oth................. t422 1 Yes 3 No 4 NA 

f. What disinfectant was used?......................................................... t423 _____________________________ 

g. What was the distance from the vehicle wash station to the selected barn in yards? 

t424 ____________yards 

8. Did workers and visitors always, sometimes, or never park in a restricted area away from the poultry barns 

during the 14-day reference period? 

a. Workers ............................................................... t425 1 Always 2 Sometimes 3 Never 

b. Visitors ................................................................. t426 1 Always 2 Sometimes 3 Never 

9. During the 14-day reference period, were wild mammals, such as raccoons, opossums, skunks, coyotes, or 

foxes, or evidence of their presence, seen in or around poultry barns? 

t427 1 Yes 3 No 

10. During the 14-day reference period, which of the following pest and wild bird control measures were used on 

this farm? 

a. Rat and mouse bait stations ........................................................................t428 1 Yes 3 No 

i. If Yes, how frequently are they checked per month? ...............................t429 __________times/month 

b. Beetle control (for example, sprays, baits, boric acid).................................t430 1 Yes 3 No 

c. Fly control (for example, baits, larvicide, space sprays/fogger, biological predators) 

..............................................................................................................t431 1 Yes 3 No 

d. Netting on barns to prevent wild bird access...............................................t432 1 Yes 3 No 

11. How often were rodents observed in the selected barn during the 14-day reference period? [Check one only.] 

t433 

1 Frequently (for example, daily) 

2 Occasionally (for example, weekly) 

3 Never 

12. What was the intensity of beetles observed in the selected barn during the 14-day reference period? [Check 

one only.] t434 

1 High 

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2 Medium 

3 Low 

4 None 

13. What was the intensity of flies observed in the selected barn during the 14-day reference period? [Check one 

only.] t435 

1 High 

2 Medium 

3 Low 

4 None 

14. Does the selected barn have a hard-surface entry pad (for example, concrete, asphalt)? 

t436 1 Yes 3 No 

If Yes, 

a. Is the entry pad cleaned? ............................................................................t437 1 Yes 3 No 

i. If Yes, specify frequency t438/t438a _______ times/ 1 week 2 month OR 3 year 

b. Is disinfectant used?....................................................................................t439 1 Yes 3 No 

15. During the 14-day reference period, how frequently were wild birds, wild animals, and rodents able to access 

poultry feed or feed ingredients (for example, feed spillage, open bag, cover left open)? 

For this question, “Always” is 100% of the time, “Most of the time” is 51-99% of the time, “Sometimes” is 1-

50% of the time, and “Never” is 0% of the time. 

Type Always Most of the time Sometimes Never 

a. Wild birds 1 2 3 4 

b. Wild animals (such as raccoons, 

opossums, skunks, coyotes, or foxes) 1 2 3 4 

c. Rodents 1 2 3 4 

t440 

t441 

t442 

16. Does this farm have a written wildlife management plan that includes methods to minimize wildlife or wild bird 

entry and reduce wildlife attractants such as standing water? t443 1 Yes 3 No 

17. In the 2 years before the 14-day reference period, were any biosecurity audits or assessments (company or 

third party) conducted on this farm? t444 1 Yes 3 No 4 Don’t know 

18. Considering the following biosecurity topics, how challenging would you say these are for producers to 

achieve? [Check one box per row.] 

Not at all 

challenging 

Slightly 

challenging 

Somewhat 

challenging 

Quite 

challenging 

Extremely 

challenging 

a. Keeping feed 

safe from 

rodents 

1 2 3 4 5 

b. Keeping feed 

safe from 

wildlife 

1 2 3 4 5 

t445 

t446 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Section E – Biosecurity Investments 

1. Over the past year, has this farm had the following ongoing biosecurity expenses? 

If Yes, what was the typical monthly cost of each? 

Biosecurity type 

Ongoing 

expenses? 

If Yes, what is the 

typical monthly 

cost? 

a. Wash station or spray area being used for 

vehicles 1 Yes 3 No $________ 

b. Foot baths 1 Yes 3 No $________ 

c. Pest and bait stations 1 Yes 3 No $________ 

d. Wash stations for employees (for example, 

sinks, showers) 1 Yes 3 No $________ 

e. PPE for employees and visitors (for example, 

gloves, coveralls, boot covers) 1 Yes 3 No $________ 

f. Other (specify:_________________) t506oth 1 Yes 3 No $________ 

Total monthly cost $________ 

t501/t507 

t502/t508 

t503/t509 

t504/t510 

t505/t511 

t506/t512 

t513 

2. Since 2015, has this farm built or made permanent improvements or renovations on the following farm 

structures that impact the farm’s biosecurity? 

a. A service room that personnel must enter through that separates “outside area” from “inside area” (for 

example, Danish entry)................................................................................t514 1 Yes 3 No 

b. Wash stations for employees (for example, sinks, showers) ......................t515 1 Yes 3 No 

c. Permanent improvements or renovations to limit wild bird access to barns t516 1 Yes 3 No 

d. Barn ventilation system ...............................................................................t517 1 Yes 3 No 

e. Other barn improvements or renovations....................................................t518 1 Yes 3 No 

f. Feed bins .....................................................................................................t519 1 Yes 3 No 

g. Permanent vehicle wash stations (for example, automated truck wash) ....t520 1 Yes 3 No 

h. Other (specify: _____________________) t521oth.......................................t521 1 Yes 3 No 

i. If Yes to any in 2a through 2h, what was the approximate total cost of all of these improvements? 

t522 $ 

3. Over the next two years, does this farm have plans to build or make permanent improvements or renovations 

on farm structures such as barns, feed bins, or other structures that impact the farm’s biosecurity? 

t523 1 Yes 3 No 

4. Since 2015, has this farm built or installed any of the following temporary structures or infrastructure that 

impact the farm’s biosecurity? 

a. Gates ...........................................................................................................t524 1 Yes 3 No 

b. Parking area ................................................................................................t525 1 Yes 3 No 

c. Temporary wild bird mitigation ....................................................................t526 1 Yes 3 No 

d. Landscape fabric on air intake inlets or curtains .........................................t527 1 Yes 3 No 

e. Temporary vehicle wash stations (for example, hand sprayer)...................t528 1 Yes 3 No 

f. Other (specify: _____________________) t529oth.......................................t529 1 Yes 3 No 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

g. If Yes to any in 4a through 4f, what was the approximate total cost of all of these improvements? 

t530 $ 

5. Over the next two years, does this farm have plans to build or install any temporary structures that impact the 

farm’s biosecurity? .............................................................................................t531 1 Yes 3 No 

6. How much did the 2014-2015 HPAI outbreak influence your decisions about biosecurity investments for this 

farm? t532 1 Not at all 2 Slightly 3 Somewhat 4 Quite a bit 5 Extremely 

Section F – Farm Help / Workers 

Questions in this section refer to persons such as the producer, employees, farm help, crews, etc. 

1. What is the total number of employees working on this farm that have access to or directly work with poultry 

(including family, both paid and unpaid)? ..........................................................t601 ___________ # 

2. Did this farm use occasional or emergency workers such as family members or part-time help to fill in for any 

employees during the 14-day reference period? ...............................................t602 1 Yes 3 No 

3. During the 14-day reference period, how frequently were the following measures used by workers entering 

the selected barn? 

For this question, “Always” is 100% of the time, “Most of the time” is 51-99% of the time, “Sometimes” is 1-

50% of the time, and “Never” is 0% of the time. N/A=not applicable. 

Measure Always Most of the time Sometimes Never N/A-Not available 

a. An established clean/dirty line 1 2 3 4 5 

b. A service room that personnel 

must enter through that separates 

“outside area” from “inside area” 

1 2 3 4 5 

c. Shower 1 2 3 4 5 

d. Wash hands or use hand 

sanitizer before entering the barn 1 2 3 4 5 

e. Wear disposable gloves 1 2 3 4 5 

f. Different personnel for different 

barns 1 2 3 4 5 

g. Locks on the barn doors 1 2 3 4 5 

h. Wear disposable coveralls 1 2 3 4 5 

i. Change of clothing/coveralls 

(washable) 1 2 3 4 5 

j. Change of shoes or use of shoe 

covers 

1 2 3 4 5 

k. Scrub footwear (bucket and 

brush) 1 2 3 4 5 

l. Foot bath (liquid) 1 2 3 4 5 

m. Foot bath (dry, such as powdered 

or particulate) 1 2 3 4 5 

t603 

t604 

t605 

t606 

t607 

t608 

t609 

t610 

t611 

t612 

t613 

t614 

t615 

[If both Question 3 l and m = not available, SKIP to Question 5.] 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

4. What was the frequency that liquid or dry footbath solutions were changed for the selected barn during the 

14-day reference period? t616/t616a _________________________________ times/ 1 week 2 month OR 3 year 

a. What disinfectant was used in the footbaths? .................. t617 ___________________________ 

5. During a typical month, do any workers on this farm visit another poultry farm? 

t618 1 Yes 3 No 4 Don’t know 

6. Are any workers or members of their household employed by other poultry operations, other company farms, 

rendering plants, or processing plants? 

a. Workers ............................................................................ t619 1 Yes 3 No 4 Don’t know 

b. Members of household ..................................................... t620 1 Yes 3 No 4 Don’t know 

7. Do any employees own their own poultry, including small backyard flocks? 

t621 1 Yes 3 No 4 Don’t know 

8. Are employees required to stay off farm after exposure to other poultry?............t622 1 Yes 3 No 

a. If Yes, for how long (hours)? ..........................................................................t623 _______ hours 

9. In a typical week, how much time is spent by all employees on biosecurity activities on the farm? 

t624 _______ hours 

10. Considering the following personnel-related topics, how challenging would you say these are for producers to 

achieve? [Check one box per row.] 

Not at all 

challenging 

Slightly 

challenging 

Somewhat 

challenging 

Quite 

challenging 

Extremely 

challenging 

a. Hiring new 

personnel 1 2 3 4 5 

b. Retaining 

trained 

personnel 

1 2 3 4 5 

c. Communicating 

the importance 

of biosecurity to 

personnel 

1 2 3 4 5 

d. Enforcing daily 

biosecurity 

measures 

1 2 3 4 5 

e. Other 

personnelrelated 

challenges 

(Specify: t629oth 

________ ) 

1 2 3 4 5 

t625 

t626 

t627 

t628 

t629 

Section G – Farm Visitors 

1. How often is a visitor log used to record visitor traffic onto the farm? 

t701 1 Always 2 Sometimes 3 Never 

2. Did any of the following types of people visit the farm during the 14-day reference period? 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

If Yes, how many times did they visit during the 14-day reference period and did they enter the selected 

barn? 

Visitor type 

Did they visit 

the farm? 

If Yes, 

How many 

times did 

they visit? 

Did this visitor 

enter the 

selected 

barn? 

a. Federal/State veterinary or 

animal health worker 1 Yes 3 No ____ # visits 1 Yes 3 No 

b. Extension agent or university 

veterinarian 1 Yes 3 No ____ # visits 1 Yes 3 No 

c. Private or company 

veterinarian 1 Yes 3 No ____ # visits 1 Yes 3 No 

d. Company service person 1 Yes 3 No ____ # visits 1 Yes 3 No 

e. Nutritionist or feed company 

consultant 1 Yes 3 No ____ # visits 1 Yes 3 No 

f. Bird delivery personnel (for 

example, poult placement, 

brood to grow move) 

1 Yes 3 No ____ # visits 1 Yes 3 No 

g. Vaccination crew 1 Yes 3 No ____ # visits 1 Yes 3 No 

h. Catch crew (bird removal) 1 Yes 3 No ____ # visits 1 Yes 3 No 

i. Artificial insemination crew (for 

breeder farms) 1 Yes 3 No ____ # visits 1 Yes 3 No 

j. Feed ingredient delivery 

person 

1 Yes 3 No ____ # visits 1 Yes 3 No 

k. Feed delivery personnel 1 Yes 3 No ____ # visits 1 Yes 3 No 

l. Egg truck personnel (for 

breeder farms) 1 Yes 3 No ____ # visits 1 Yes 3 No 

m. Fresh litter delivery services 1 Yes 3 No ____ # visits 1 Yes 3 No 

n. Litter removal services (for 

example, litter broker, litter 

disposal) 

1 Yes 3 No ____ # visits 1 Yes 3 No 

o. Customer (private individual) 1 Yes 3 No ____ # visits 1 Yes 3 No 

p. Wholesaler, buyer, or dealer 1 Yes 3 No ____ # visits 1 Yes 3 No 

q. Renderer 1 Yes 3 No ____ # visits 1 Yes 3 No 

r. Dead bird pickup other than by 

renderer 1 Yes 3 No ____ # visits 1 Yes 3 No 

s. Rodent control crew 1 Yes 3 No ____ # visits 1 Yes 3 No 

t. Occasional worker (for 

example, family member, parttime help over holiday) 

1 Yes 3 No ____ # visits 1 Yes 3 No 

u. Construction workers, repair or 

maintenance personnel 1 Yes 3 No ____ # visits 1 Yes 3 No 

v. Other business visitors 

(including other producers, 1 Yes 3 No ____ # visits 1 Yes 3 No 

t702/t725/t748 

t703/t726/t749 

t704/t727/t750 

t705/t728/t751 

t706/t729/t752 

t707/t730/t753 

t708/t731/t754 

t709/t732/t755 

t710/t733/t756 

t711/t734/t757 

t712/t735/t758 

t713/t736/t759 

t714/t737/t760 

t715/t738/t761 

t716/t739/t762 

t717/t740/t763 

t718/t741/t764 

t719/t742/t765 

t720/t743/t766 

t721/t744/t767 

t722/t745/t768 

t723/t746/t769 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

meter readers, package 

delivery (UPS), propane, or 

similar) 

w. Other nonbusiness visitors 

(including neighbors, family 

members, friends, and school 

field trips) 

1 Yes 3 No ____ # visits 1 Yes 3 No t724/t747/t770 

3. For those visitors who entered the selected barn during the 14-day reference period, did you require the 

following? [Check one per row.] 

Yes, verified 

at farm 

Yes, visitor 

responsibility No 

a. Change of outer clothing/farm specific 

clothing/coveralls 1 2 3 

b. Foot covers or change of footwear 1 2 3 

c. Mask 1 2 3 

d. Hand sanitizing or handwashing 1 2 3 

e. Gloves 1 2 3 

f. Not visit multiple farms in the same day 1 2 3 

g. Other (specify: ________________ ) 

t777oth 

1 2 3 

t771 

t772 

t773 

t774 

t775 

t776 

t777 

4. How often is a restroom facility (including portable) available to crews that visit the farm? 

t778 1 Always (24 hours/day) 2 Sometimes 3 Never 

Section H – Farm Vehicles and Equipment 

1. Were the following vehicles shared with another farm during the 14-day reference period? 

If Yes, how often were they cleaned and disinfected prior to returning to this farm? 

Vehicle type 

Shared with 

another farm in the 

14-day reference 

period? 

If Yes, how often 

was it cleaned 

and disinfected 

prior to returning 

to this farm? 

a. Company trucks or trailers (for example, 

pickup truck, trailer with supplies, 

supervisor truck, or similar) 

1 Yes 3 No 

1 Always 

2 Sometimes 

3 Never 

b. Feed trucks 1 Yes 3 No 

1 Always 

2 Sometimes 

3 Never 

c. Feed ingredient truck 1 Yes 3 No 

1 Always 

2 Sometimes 

3 Never 

t801/t810 

t802/t811 

t803/t812 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

d. Bird delivery vehicles (for example, placing 

birds) 1 Yes 3 No 

1 Always 

2 Sometimes 

3 Never 

e. Bird removal vehicles (for example, moved 

to slaughter, moved to grow) 1 Yes 3 No 

1 Always 

2 Sometimes 

3 Never 

f. Egg removal vehicles (for breeder farms) 1 Yes 3 No 

1 Always 

2 Sometimes 

3 Never 

g. Manure/litter hauling 1 Yes 3 No 

1 Always 

2 Sometimes 

3 Never 

h. ATV/4-wheeler 1 Yes 3 No 

1 Always 

2 Sometimes 

3 Never 

i. Other (specify:______________________) 

t809oth 

1 Yes 3 No 

1 Always 

2 Sometimes 

3 Never 

t804/t813 

t805/t814 

t806/t815 

t807/t816 

t808/t817 

t809/t818 

2. Were the following pieces of equipment shared with another farm during the 14-day reference period? 

If Yes, how often were they cleaned and disinfected prior to returning to this farm? 

Equipment type 

Shared with 

another farm in the 

14-day reference 

period? 

If Yes, how often 

was it cleaned 

and disinfected 

prior to returning 

to this farm? 

a. Gates/panels 1 Yes 3 No 

1 Always 

2 Sometimes 

3 Never 

b. Lawn mowers 1 Yes 3 No 

1 Always 

2 Sometimes 

3 Never 

c. Live haul loaders 1 Yes 3 No 

1 Always 

2 Sometimes 

3 Never 

d. Catch pens 1 Yes 3 No 

1 Always 

2 Sometimes 

3 Never 

e. Scales for weighing birds 1 Yes 3 No 

1 Always 

2 Sometimes 

3 Never 

t819/t830 

t820/t831 

t821/t832 

t822/t833 

t823/t834 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

f. Vaccination equipment 1 Yes 3 No 

1 Always 

2 Sometimes 

3 Never 

g. Pressure sprayers/washers/foamers 1 Yes 3 No 

1 Always 

2 Sometimes 

3 Never 

h. Skid-steer loaders 1 Yes 3 No 

1 Always 

2 Sometimes 

3 Never 

i. Litter/manure handling 1 Yes 3 No 

1 Always 

2 Sometimes 

3 Never 

j. Tillers/de-caking equipment 1 Yes 3 No 

1 Always 

2 Sometimes 

3 Never 

k. Other (specify:______________________) 

t829oth 

1 Yes 3 No 

1 Always 

2 Sometimes 

3 Never 

t824/t835 

t825/t836 

t826/t837 

t827/t838 

t828/t839 

t829/t840 

3. Considering the following equipment-related topics, how challenging would you say these are for producers to 

achieve? [Check one box per row.] 

Not at all 

challenging 

Slightly 

challenging 

Somewhat 

challenging 

Quite 

challenging 

Extremely 

challenging 

a. Keeping shared 

vehicles 

cleaned and 

disinfected 

1 2 3 4 5 

b. Keeping shared 

small 

equipment 

(such as catch 

pens or litter 

tillers) cleaned 

and disinfected 

1 2 3 4 5 

c. Other 

equipment or 

vehicle-related 

challenges 

(Specify: t843oth 

_______________) 

1 2 3 4 5 

t841 

t842 

t843 

Section I – Litter Handling 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

1. Was fresh litter/bedding brought onto the farm during the 14-day reference period? 

t901 1 Yes 3 No 

a. If Yes, who brought the fresh litter onto the farm? [Check one only.] t902 

1 Company personnel 

2 Litter provider 

3 Other (specify: _____________________ ) t902oth 

2. Is the fresh litter heat treated prior to delivery? t903 1 Yes 3 No 4 Don’t know 

3. Prior to use, is fresh litter stored on the farm: 

a. Outside ........................................................................................................t904 1 Yes 3 No 

i. If Yes, is it covered?..............................................................................t905 1 Yes 3 No 

b. In a shed .....................................................................................................t906 1 Yes 3 No 

i. If Yes, is the shed closed? ....................................................................t907 1 Yes 3 No 

[If both Questions 3 a and b = No, SKIP to Question 6.] 

4. What is the distance (in yards) from the on-site fresh litter storage area to the selected barn? 

..............................................................................................................t908 ________ yards 

5. Prior to use, is fresh litter accessible to: 

a. Wild birds .....................................................................................................t909 1 Yes 3 No 

b. Wild animals (for example, raccoons, opossum, coyotes, foxes) ...............t910 1 Yes 3 No 

c. Domestic animals (for example, dogs, cats) ...............................................t911 1 Yes 3 No 

6. What was the date that used litter was last removed from any barn on this farm prior to the end of the 14-day 

reference period? ................................................................. .............................t912 ________ mm/dd/yy 

7. How was used litter disposed of prior to or during the 14-day reference period? 

a. Composted on-farm.....................................................................................t913 1 Yes 3 No 

i. If Yes, what is the distance (in yards) to the selected barn?...............t914 _______ yards 

b. Stored on-farm.............................................................................................t915 1 Yes 3 No 

c. Applied to land on this farm .........................................................................t916 1 Yes 3 No 

i. If Yes, what was the date litter was applied to land? ............................t917 _______ mm/dd/yy 

d. Taken off-site...............................................................................................t918 1 Yes 3 No 

8. Was manure or used litter from other farms brought onto this farm or adjacent farms prior to or during the 

reference period? t919 1 Yes 3 No 4 Don’t know 

9. How many times was fresh litter added to the selected barn during the reference period? 

t920 ________ times 

These next three questions ask about the litter management practices for the selected barn around the 

time of the 14-day reference period. 

10. Was litter “tilled” after it was placed in the selected barn? ................................... t921 1 Yes 3 No 

11. Was there a partial clean out of the selected barn?............................................. t922 1 Yes 3 No 

12. When was the last full clean out of the selected barn? [Check one only.] t923 

1 Prior to this flock 

2 Two flocks ago 

80 USDA APHIS 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

3 Three or more flocks ago 

Section J – Dead Bird Disposal 

1. What is the approximate normal daily mortality on this farm? ............................... t1001 __________#/day 

2. During the 14-day reference period, what were the method(s) of dead bird (daily mortality) disposal on this 

farm? 

a. Composting..................................................................................................t1002 1 Yes 3 No 

b. Burial............................................................................................................t1003 1 Yes 3 No 

c. Incineration ..................................................................................................t1004 1 Yes 3 No 

d. Rendering ....................................................................................................t1005 1 Yes 3 No 

e. Landfill .........................................................................................................t1006 1 Yes 3 No 

f. Other (specify: ____________________ ) t1007oth.......................................t1007 1 Yes 3 No 

3. If Question 2a (composting) or Question 2b (burial) is Yes, how frequently are carcasses covered with: 

a. Soil?...............................................................t1008 1 Daily 2 Every 2 or more days 3 Never 

b. Manure?.........................................................t1009 1 Daily 2 Every 2 or more days 3 Never 

4. If Question 2d (rendering) is Yes, 

a. Is the carcass bin kept covered?.................................................................t1010 1 Yes 3 No 

b. Are carcasses: [Check one only.] t1011 

1 Taken by the producer or worker to the renderer? 

2 Picked up by the renderer from the farm? 

c. How many times were carcasses moved to the renderer during the 14-day reference period? 

t1012 _________ # times 

5. Does this farm have an alternative mortality disposal plan if the typical method is disrupted, and carcasses 

cannot be moved off farm? .................................................................................... t1013 1 Yes 3 No 

6. Were any wild birds or wild mammals observed around the dead bird collection area (such as burial, compost 

pile, rendering bin, or similar) during the 14-day reference period? 

a. Wild birds ......................................................................................................... t1014 1 Yes 3 No 

b. Wild mammals ................................................................................................. t1015 1 Yes 3 No 

7. During the 14-day reference period, did this farm use a shared collection point for dead bird disposal? [Check 

one only.] t1016 1 Yes – located on this farm 2 Yes – located off this farm 3 No 

8. How far is the selected barn (in yards) from the dead bird disposal/holding area including carcass bin for 

rendering? t1017......................................................................................................................... yards 

Section K – Selected Barn Characteristics 

Answer this entire section for the selected barn that was chosen in Section B. Answer questions for the 14-day 

reference period. 

1. Which best describes the ground surface immediately surrounding (within 1 yard) this barn (excluding vehicle 

approach and loading area)? [Check one only.] t1101 

1 Gravel or hard surface 

2 Dirt 

3 Short grass 

81 USDA APHIS 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

4 Tall grass or brush 

2. Were the following type(s) of poultry present in this barn during the 14-day reference period? 

a. Brooder ............................................................................................................ t1102 1 Yes 3 No 

b. Grower toms .................................................................................................... t1103 1 Yes 3 No 

c. Grower hens .................................................................................................... t1104 1 Yes 3 No 

d. Breeders .......................................................................................................... t1105 1 Yes 3 No 

e. Other (specify: __________________________ ) t1106oth.............................. t1106 1 Yes 3 No 

3. For the flock that was present during the 14-day reference period, how many birds were placed in this barn? 

t1107 ........................................................................................................................# birds 

4. What was the date of placement in this barn?...................................................t1108 _________ mm/dd/yy 

5. How old were birds when placed in this barn?..t1109d ___________days OR t1109w _____________ weeks 

6. Were different stages of production (for example, brooders and growers) present in this barn at the same time 

during the 14-day reference period?...................................................................... t1110 1 Yes 3 No 

7. Was there a partial load-out of this barn during the reference period? ................. t1111 1 Yes 3 No 

8. Was there another health concern in this flock during the reference period? ....... t1112 1 Yes 3 No 

a. If Yes, specify condition: t1113 ___________________________________ 

9. Was this flock being treated for a condition or health concern during the reference period? 

t1114 1 Yes 3 No 

a. If Yes, specify treatment: t1115___________________________________ 

10. How old is this barn structure?............................................................................... t1116 ________years 

11. How long has it been since the last remodel of the barn structure?...................... t1117 ________years 

t1117a 1 NA – Never remodeled 

12. How well has the barn structure been maintained? [Check one only.] t1118 

1 Well – For example, walls, curtains, and mud boards do not have holes, no visible daylight, the barn is 

tight and well insulated 

2 Moderate – For example, barn could have rust or small holes, mud boards may be damaged, curtains 

may be torn or not in good repair, curtains may not close all the way, insulation may not be in good repair, the 

poly may be hanging from the ceiling 

3 Poor – For example, holes in walls and mud boards are apparent, tin is rusted, may have leaks in roof, 

there might be some holes large enough for wild birds to enter, multiple areas with daylight visible, insulation 

may be hanging from the ceiling 

13. Is this barn bird proof? ........................................................................................... t1119 1 Yes 3 No 

14. During the 14-day reference period, did you notice any water seepage into the barn (for example, water 

entering the barn from snowmelt or rainwater)? .......................... t1120 1 Yes 3 No 4 Don’t know 

15. What type of ventilation was used for this barn during the 14-day reference period? [Check one only.] t1121 

1 Curtain ventilated 

2 Environmental control/tunnel ventilation 

3 Side doors (such as tip outs) 

4 Other (specify: ____________________ ) t1121oth 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

16. During the 14-day reference period, 

a. What percentage of time were the curtains open? t1122/t1133 __________ % time 4 Don’t know 

b. How many days were the curtains open or partially open? t1123 /t1134 _____ # days 4 Don’t know 

17. Was intake air filtered during the 14-day reference period?.................................. t1124 1 Yes 3 No 

a. If Yes, specify type of filter: t1125 _________________________________ 

18. During the 14-day reference period, was landscape fabric in place on either air intake inlets or along curtains 

on the barn? 

a. On air intake inlets........................................................................................... t1126 1 Yes 3 No 

b. Along curtains .................................................................................................. t1127 1 Yes 3 No 

[If both Question 18a and 18b = No, SKIP to Question 21.] 

19. During the 14-day reference period, was any of this landscape fabric installed or replaced on either air intake 

inlets or along curtains? ......................................................................................... t1128 1 Yes 3 No 

20. During the 14-day reference period, was any of this landscape fabric sprayed with disinfectant on either air 

intake inlets or along curtains?............................................................................... t1129 1 Yes 3 No 

a. If Yes, how often was it sprayed: ............................. t1130/t1130a ____times / 1 day OR 2 week 

21. How frequently were the following used in this barn during the 14-day reference period? [Check one per row.] 

Used regularly Not used regularly Not available 

a. Cool cell pads 1 2 3 

b. Misters 1 2 3 

t1131 

t1132 

Section L – Office Use Only 

1. Interview response code. [Check only one.] t1201 

1 Survey completed 

2 Refused 

3 Out of business 

4 No turkeys present during 2022 

5 Inaccessible 

6 Other (specify: ____________________ ) t1201oth 

Comment Section 

Please use this section for anything else that you would like to add. For example, how do you think HPAI was/is 

spreading within your geographic area? t1301 

83 USDA APHIS 
 

 

 

 

Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

APPENDIX D: H5N1 HPAI BIRD DETECTIONS 

Table D1. Number of H5N1 HPAI detections in apparently healthy and sick/dead birds from 30 December 2021 to 31 

March 2023. 

Species # HPAI Detections in Apparently # HPAI Detections in Sick/Dead 

Healthy Birds Birds 

American black duck 42 0 

American coot 0 2 

American crow 0 58 

American green-winged teal 392* 3 

American kestrel 0 1 

American robin 0 1 

American white pelican 1 90 

American wigeon 232* 2 

American wood stork 0 2 

Arctic tern 0 2 

Bald eagle 0 344 

Barn owl 0 1 

Barred owl 0 10 

Black skimmer 0 2 

Black turnstone 0 1 

Black vulture 0 546 

Black-billed magpie 0 3 

Black-crowned night heron 0 5 

Black-legged kittiwake 0 1 

Blue-winged teal 385* 7 

Boat-tailed grackle 0 1 

Bonaparte's gull 0 1 

Brant 0 7 

Brown pelican 0 12 

Bufflehead 1 8 

Cackling goose 0 17 

California condor 0 1 

California gull 0 2 

Canada goose 6 556 

Caspian tern 0 13 

Cinnamon teal 17* 2 

Common eider 0 28 

Common goldeneye 2 4 

Common grackle 0 2 

Common loon 0 8 

Common merganser 0 2 

Common raven 0 32 

Common tern 0 11 

Cooper's hawk 0 16 

Cormorant (unidentified) 0 8 

Crested caracara 0 1 

Crow (unidentified) 0 4 

Double-crested cormorant 0 26 

Duck (unidentified) 0 12 

Dunlin 0 3 

84 USDA APHIS 
 

 

Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Species # HPAI Detections in Apparently # HPAI Detections in Sick/Dead 

Healthy Birds Birds 

Eagle (unidentified) 0 1 

Eared grebe 0 13 

Eastern screech owl 0 3 

Eider (unidentified) 0 1 

Ferruginous hawk 0 1 

Fish crow 0 5 

Forster's tern 0 1 

Fulvous whistling duck 1 0 

Gadwall 186* 11 

Gannet 0 1 

Glaucous gull 0 12 

Glossy ibis 0 1 

Golden eagle 0 3 

Goose (unidentified) 0 79 

Great black-backed gull 0 28 

Great blue heron 0 9 

Great egret 0 3 

Great horned owl 0 192 

Greater sage grouse 0 1 

Greater scaup 0 1 

Greater white-fronted goose 0 16 

Great-tailed grackle 0 3 

Green heron 0 1 

Gull (unidentified) 0 24 

Harris hawk 0 1 

Hawk (unidentified) 0 21 

Heron (unidentified) 0 1 

Herring gull 0 36 

Hooded merganser 1 22 

Horned grebe 0 2 

House sparrow 0 1 

Laughing gull 0 1 

Lesser scaup 5* 27 

Long-eared owl 0 1 

Magpie (unidentified) 0 2 

Mallard 750* 69 

Merganser (unidentified) 0 6 

Merlin 0 1 

Mottled duck 1 0 

Muscovy duck 0 31 

Mute swan 1 18 

Neotropic cormorant 0 3 

Northern fulmar 0 1 

Northern gannet 0 2 

Northern harrier 0 2 

Northern pintail 51* 4 

Northern shoveler 82 0 

Osprey 0 2 

Owl (unidentified) 0 11 

Pacific loon 0 1 

85 USDA APHIS 
 

 

Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Species # HPAI Detections in Apparently # HPAI Detections in Sick/Dead 

Healthy Birds Birds 

Parasitic jaeger 0 2 

Pelican (unidentified) 0 9 

Peregrine falcon 0 38 

Pheasant (unidentified) 0 3 

Pied-billed grebe 0 1 

Prairie falcon 0 1 

Redhead duck 3 9 

Red-necked grebe 0 1 

Red-necked phalarope 0 1 

Red-shouldered hawk 0 8 

Red-tailed hawk 0 221 

Red-winged blackbird 0 1 

Ring-billed gull 0 5 

Ring-necked duck 2 8 

Roseate spoonbill 0 1 

Ross's goose 17 85 

Rough-legged hawk 0 5 

Royal tern 0 3 

Ruddy turnstone 0 1 

Ruffed grouse 0 1 

Sabine's gull 0 3 

Sanderling 0 17 

Sandhill crane 0 10 

Sandwich tern 0 1 

Sharp-shinned hawk 0 5 

Short-billed gull 0 1 

Short-eared owl 0 1 

Snow goose 93* 419 

Snowy egret 0 2 

Snowy owl 0 15 

Snowy plover 0 4 

Swainson's hawk 0 6 

Swan (unidentified) 0 11 

Thayer's gull 0 1 

Tree swallow 0 1 

Trumpeter swan 0 18 

Tundra swan 1 9 

Turkey vulture 0 99 

Vulture (unidentified) 0 2 

Western grebe 0 1 

Western gull 0 7 

Western screech owl 0 2 

White-faced ibis 0 1 

White-winged scoter 0 1 

Wild turkey 0 17 

Willet 0 1 

Wood duck 174 37 

Grand Total 2,446* 3,639 

*Includes apparently healthy bird samples collected by other agencies 

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Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

APPENDIX E: TIME OF INTRODUCTION MODELING METHODS 

We used approximate Bayesian computation (ABC) to estimate the likely time of virus introduction and key 

model parameters, such as the adequate contact rate––a parameter which regulates the rate of within-flock 

disease spread––from the available production and test data. 

A stochastic individual-based simulation model was first used to simulate the disease mortality, infection 

prevalence over time, and water consumption (where applicable) over a wide range of values for model 

parameters, such as the adequate contact rate, times of disease introduction, and bird-level latent and 

infectious period distributions (i.e., prior distributions). 

In the next step, the sum of the squared distance between the model-predicted daily mortality and water 

consumption (where applicable) and the observed data, and the difference between observed and 

simulated diagnostic test results, was calculated as a measure of deviation between the model output and 

data (ψ). The parameters in model iterations where the metric ψ was sufficiently small, indicating a good fit 

to the data, were then accepted to estimate the distribution of the time of introduction and other model 

parameters. 

We used wide priors for input variables based on published literature and estimates from previous SEPRL 

challenge studies. Preliminary data from SEPRL challenge studies in turkeys and chickens with a current 

outbreak isolate (A/American Widgeon/SC/22-000345-001/2022 (H5N1) HPAIV) were made available in May 

2022. We estimated the disease state durations from the challenge study data using Markov chain Monte 

Carlo algorithms. The estimated disease state durations were then used to update the prior distributions for 

the latent and infectious periods. The updated prior distributions used in the analysis for WOAH poultry 

[commercial] meat turkey and table egg layer flocks based on SEPRL data and other published studies are 

summarized in Table E1 and Table E2, respectively. We also performed a sensitivity analysis for the impact 

of the mean infectious period prior for selected premises given the uncertainty in this parameter. 

Table E1. Input prior distribution parameters used in the ABC approach to estimate the adequate contact rate and time 

of virus introduction for WOAH poultry [commercial] meat turkey flocks. 

Parameter Name Description Distribution 

Adequate Contact Rate Daily average number of contacts a 

bird has with other birds that are 

sufficient to transmit infection 

Uniform (min = 0.2, max = 7) per 

day 

Latent Period Length Distribution Length of the interval when a bird 

is latently infected and is not 

infectious 

Gamma (shape = 4.037, scale = 

0.1809); mean = 0.64 days; 

variance = 0.67 

Mean Infectious Period Prior distribution for the mean 

infectious period 

Uniform (1.9 – 6.3 days) 

Shape Parameter for Infectious 

Period 

Prior distribution for the shape 

parameter of gamma distributed 

infectious period 

Uniform (1 – 20) 

87 USDA APHIS 
 

 

 

 

Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Table E2. Input prior distribution parameters used in the ABC approach to estimate the adequate contact rate and time 

of virus introduction for WOAH poultry [commercial] table egg layer flocks. 

Parameter Name Description Distribution 

Adequate Contact Rate 

Latent Period Length Distribution 

Mean Infectious Period 

Shape Parameter for Infectious 

Period 

Daily average number of contacts a 

bird has with other birds that are 

sufficient to transmit infection 

Length of the interval when a bird 

is latently infected and is not 

infectious 

Prior distribution for the mean 

infectious period 

Prior distribution for the shape 

parameter of gamma distributed 

infectious period 

Uniform (min = 0.5, max = 9) per 

day 

Gamma (shape = 2.54, scale = 

0.33); mean = 0.8 4 days; variance = 

0.67 

Uniform (0.74 – 4 days) 

Uniform (1 – 20) 

88 USDA APHIS 
 

 

 

 

Epidemiologic and Other Analyses of HPAI Affected Poultry Flocks 1 June 2023 

Epidemiologic and Other Analyses of HPAI Affected Poultry 

Flocks 

1 June 2023 Report 

USDA  APHIS  VS 

Center for Epidemiology and Animal Health 

2150 Centre Avenue, Bldg. B, Fort Collins, CO, 80526-8117 

Web: http://www.aphis.usda.gov/animal-health/ceah 

89 USDA APHIS